Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AE015451	3,951,159	T→C	intergenic (‑123/+72)	PP_3486 ← / ← PP_3487	putative cytochrome c/conserved exported protein of unknown function

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AE015451	3,951,159	0	T	C	94.7%	57.7 / NA	19	intergenic (‑123/+72)	PP_3486/PP_3487	putative cytochrome c/conserved exported protein of unknown function
Reads supporting (aligned to +/- strand):  ref base T (0/0);  major base C (12/6);  minor base G (0/1);  total (12/7)
Fisher's exact test for biased strand distribution p-value = 3.68e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

GGCAGCACGCTGGCGGGGACTGTGATATCGCTGGCGCCGACCCGGGCTTGCAATTGAGCGTCGC‑TACTGGAGACGCCCTCGCGGTAAAGGCGTTTGCCTGCTTGTTCGTGGTCGGTCAGGTCCAGGGCCAGGGCTGAGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCTTATCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGAATCTTGCTCCAGCGTTTACCTGCAACATCACCGGCAATCAGCTGCGTCGAATGCTGCTCGGGACTCGGCAGGAACTGCCCTATACGGCCAAGCACCAGGTCGACATTGGCCTTGTCGCCGGTCAGGAACAGCCAGTTCGG  >  AE015451/3950885‑3951443                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                                                              ggCAGCACGCTGGCGGGGACTGTGATATCGCTGGCGCCGACCCGGGCTTGCAATTGAGCGTCGC‑TACTGGAGACGCCCTCGCGGTAAAGGCGTTTGCCTGCTTGTTCGTGGTCGGTCAGGTCCAGGGCCAGGGCTGAGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCca‑ca                                                                                                                                                                                                                                                                    >  1:96582/1‑301 (MQ=255)      caCGCTGGCGGGGACTGTGATAGCGCTGGCGCCGAACCGGGTTTGGCATTGAGCG‑GGCGTACTGGAGGCGCCCGCGCGGTAAAGGCGTTTGCCTGCGTGTTCGTGGTCGGTCAGGTCCAGGGCCGGGGCTGAGGTCGAGGTTGCCATGCCAAGCCCGCAGGTAGGCCATATCGCAAGCCCTGGGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGc                                                                                                                                                                                                                                                               <  2:357780/301‑1 (MQ=255)           ggggggggCCTGTGATACCGCGGGCGCCGACCCGGGCGTGCAATTGAGCGTCGC‑TACTGGAGACGCCCTGGCGGTAAAGGCGTTTGCCTGCTTGTTCGTGGTCGGTCAGGTCCAGGGCCAGGGCTGAGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAGGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATg                                                                                                                                                                                                                                                          <  1:28277/297‑1 (MQ=255)                                         cccgggtggtcAATTGAGCATCGC‑TATTGGGGACGCCTGAGCGGTAAAGTGGTTTGCCGGCTTGTTCTGGGTCGGTCAGGTGCAGGGCAAGGGCTGAGGTCGAAGTGGCAAGGCCAAGCACGCAGGTAAGCCATAGCGCACGCCCGGTGGGAGCGGCCGTGCGGCGCGAAAGGGCTGCCCAGCAGCCCCGGCAGTGGCAGCGCAAGCGCAGAAAGAGGGGGGCGCTGCGCGCTCGTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCAt                                                                                                                                                                                                                            <  2:236746/291‑1 (MQ=255)                                         cccGGGCTTGGAATTGGGCGTCGC‑CACTGGAGATGCCCTGGCGGTAATGGCGTTTGCCTGGTTGTTCGTGGTCGGTCAGGTCAAGGGCCAGGGCTGAGGTCGAAGTTGCAATGCAAAGCACGAAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCAt                                                                                                                                                                                                                            <  1:414076/301‑1 (MQ=255)                                          ccGGGCTTGCAATTGAGCGTCGC‑TACTGGAGACGCCCTCGCGGTAAAGGCGTTTGCCTGCTTGTTCGTGGTCGGTCAGGTCCAGGGCCAGGGCTGAGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCCCCGCAAGGCCGCCCCCA‑CAAAAGCGGATGCCACCGAGGCCAATTCCCCAggcctaccatc                                                                                                                                                                                                                           >  1:411856/1‑293 (MQ=255)                                                              cGC‑TACTGGGGACGCCCGCGCGGTAAAGGCGTTTGCCTGCTTGTTCGTGGTCGGTCAGGTCCAGGGCCAGGGCTGAGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGc                                                                                                                                                                                                       <  2:96544/301‑1 (MQ=255)                                                                  tACTGGAGACGCCCTCGCGGTAAAGGCGTTTGCCTGCTTGTTCGTGGTCGGTCAGGTCCAGGGCCAGGGCTGAGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCCAGGCCGC‑CCCACCAAAAGCAGATGCCACCGTGGCTAATTCCCCACGCGGCCCCTGATACCCcccgactcgcacgcgcc                                                                                                                                                                                                    >  2:50464/1‑290 (MQ=255)                                                                            cctctggctgTAAAGGCGTGGGCCTGCTTGTTCGTGGCTGGTGAGTTCCAGGGCCAGGGCTGATGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGACATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGAGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACa                                                                                                                                                                                          <  1:281803/292‑1 (MQ=255)                                                                                gcggggcaaaGGCGTTTGCTGGCGTGGTCGTGGTCGGTCAGGCGCAGGGCCAGGGCTGAGGTCGAAGTTGCCAGGCCAAGCACGCAGGTACGCCAGATCGCAAGCCCTGGGGGAGCGGCCGTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGCGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTg                                                                                                                                                                                      <  1:265766/294‑1 (MQ=255)                                                                                                                       aGGTCCAGGGCCAGGGCTGAGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCCGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCACCAGGCAGCCCATGATACCCACCGACCGGCCAGCGGCCGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTTGCGGTGCATCCGTGCg                                                                                                                                               >  1:562835/1‑301 (MQ=255)                                                                                                                                                     gccatgccaAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAATGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAACGAGGAGGCCACAGAGGCCAATTCCCCAGGCGGCGCATGAGACTCACCGAACGGCCAGCGGCTGGGTCAACAGCAGCATGCGTTGGGCAATCGTCGCGGGCGGTGCATCCGGGCGAATCTTGCGCCGGCGTTGACTTGCAACAta                                                                                                                 >  1:57395/1‑300 (MQ=255)                                                                                                                                                         tgccaAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGGTGGCGGTTCATCCGGGCGAATCTTGCTCCAGCGTTTACCTGCAACATCAccc                                                                                                             >  1:416763/1‑300 (MQ=255)                                                                                                                                                                                                   cGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCTGCTGGGTCAACAGCTGCATTCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGAATCTTGCTCCAGCGTTTACCTGCAACATCCCCGGCAATCAGCTGCGTCGTATGCTGCCCGGGACTCGGCAGGAAc                                                                   >  1:384182/1‑301 (MQ=255)                                                                                                                                                                                                      ccTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGAATCTTGCTCCAGCGTTTACCTGCAACATCACCGGCAATCAGCTGCGTCGAATGCTGCTCGGGACTCGGCAGGAACTGc                                                                >  1:398505/1‑301 (MQ=255)                                                                                                                                                                                                            gTCGCGAAAGGGCTGTGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGAATCTTGCTCCAGCGTTTACCTGCAACATCACCGGCAATCAGCCGCGTCGAATGCTGCTCGGGACTCGGCAGGAACTGCCCtata                                                          >  2:649562/1‑301 (MQ=255)                                                                                                                                                                                                                        cTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGTCGAATCTTGCTCCAGCGTTTACCTGCCACATCACCGGCAATCCGCTTCGTCGCATGCTGCCCGGGACTCGGCAGGCACTGCCCTCTACGGCCAAGCAcc                                              >  2:689652/1‑301 (MQ=255)                                                                                                                                                                                                                                                                  ggggAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGAATCTTGCTCCAGCGTTTACCTGCAACATCACCGGCAATCAGCTGCGTCGAATGCTGCTCGGGACTCGGCAGGAACTGCCCTATACGGCCAAGCACCAGGTCGACATTGGCCTTGTCGCCGGTCAGGACCAGCCCGTTc    >  2:309058/1‑301 (MQ=255)                                                                                                                                                                                                                                                                    ggAGCGCTGCGCGCTCCTTTCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGAATCTTGCTCCAGCGTTTACCTGCAACATCACCGTCACTCAGCTTCCTCGCACGCTCCTCGGGACTCGTCAGGAACTTCCCTATACGGCCAAGCACCGGGTCCCTATTGGCCTTCTCCCCTCTCCGGAACAGcccattcgc  >  2:504338/1‑294 (MQ=255)                                                                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                                                              GGCAGCACGCTGGCGGGGACTGTGATATCGCTGGCGCCGACCCGGGCTTGCAATTGAGCGTCGC‑TACTGGAGACGCCCTCGCGGTAAAGGCGTTTGCCTGCTTGTTCGTGGTCGGTCAGGTCCAGGGCCAGGGCTGAGGTCGAAGTTGCCATGCCAAGCACGCAGGTAAGCCATATCGCAAGCCCTGTGGGAGCGGCCTTGCGTCGCGAAAGGGCTGCGCAGCAGCCCCGGCAGTGGCAGCTCAAGCGCAGAAAGAGGGGAGCGCTGCGCGCTCTTATCGCGACGCAAGGCCGCTCCCA‑CAAAAGCGGATGCCACAGAGGCCAATTCCCCAGGCGGCCCATGATACTCACCGACCGGCCAGCGGCTGGGTCAACAGCTGCATGCGCTGGGCAATCGCCGCTGGCGGTGCATCCGGGCGAATCTTGCTCCAGCGTTTACCTGCAACATCACCGGCAATCAGCTGCGTCGAATGCTGCTCGGGACTCGGCAGGAACTGCCCTATACGGCCAAGCACCAGGTCGACATTGGCCTTGTCGCCGGTCAGGAACAGCCAGTTCGG  >  AE015451/3950885‑3951443

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑