Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,275,084	G→C	14.3%	intergenic (‑281/+31)	PP_5462 ← / ← PP_5463	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,275,084	0	G	C	14.3%	58.7 / 4.4	28	intergenic (‑281/+31)	PP_5462/PP_5463	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (14/10);  new base C (2/2);  total (16/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.43e-01

TGCGAATGGGCATTTTGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTATCCAGCCTGTTC  >  NC_002947/1274940‑1275231                                                                                                                                                 |                                                                                                                                                    tGCGAATGGGCATTTTGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGAttg                                                                                                                                                 >  6:53123/1‑147 (MQ=255)     aaTGGGCATTTTGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATgggcgg                                                                                                                                             <  1:241053/149‑1 (MQ=255)       tGGGCATTTTGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATgggcgggc                                                                                                                                           <  5:53123/149‑1 (MQ=255)          gCATTTTGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCCATCGGCGGGCttt                                                                                                                                        <  4:131386/149‑2 (MQ=255)          gCATTTTGGTCTATCCGGCGGAGAGTGAATCTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCtt                                                                                                                                         >  1:32969/1‑148 (MQ=255)             ttttGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAgg                                                                                                                                     >  7:289311/1‑149 (MQ=255)                  ttCTATCCGGCGTAGAGTGAATGTGGTAGCCTGCTTCCCGGTTACGTCGGATCCAATAAGGTGCGGGAGAGCTGTAATGATGGGGGTTATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAgggggg                                                                                                                                 <  8:145257/147‑1 (MQ=255)                  gTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAggggtgg                                                                                                                                >  7:386681/1‑149 (MQ=255)                                 cgTGAACGTCCAAGCCTGCTTCCCGGGTACGTCGGCTCCAATAAGCTGCGGGAGAGCGGGAATGATGCGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCg                                                                                                                 <  8:386681/148‑1 (MQ=255)                                                cTGCTTCCCGCTTACGTCGGCTCCACTACGCGGCGGGAGAGCCGTAATGATGGGCGCGATCGTGGTAAAGGCGAAACGACAACGACCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTACCGTACTACGGTCGCTtc                                                                                                  <  2:32969/149‑1 (MQ=255)                                                  gcagcccGGTGACGGCGCCTCCAATAAGGTGCGGGAGAGCGGGAATGATGGGTGTGCTGGTGGTCAAGGTGACAGGAGACTGAGCAAAGCCCGCCGATGGGCGGGCTTCAGGGGTGGGCAGAAGGGCTATCGTACTACGGTCGCTtctc                                                                                                <  8:289311/145‑1 (MQ=255)                                                  gCTTCCCGCTTACCTCGGCTCCAATACCGTGCGGGAGAGCGGTAACGAGGGGGGGCATGGCGCAAAAGGGCAACGGAGAATGCGCCACGCCCCCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTtctc                                                                                                <  4:204440/149‑1 (MQ=255)                                                    ttCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCGTCTCGt                                                                                              >  4:205839/1‑149 (MQ=255)                                                     tCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATgggcgggc                                                                                                                                           >  4:101866/1‑103 (MQ=255)                                                     tCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATgggcgggc                                                                                                                                           <  3:101866/103‑1 (MQ=255)                                                                tCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAgg                                                                                   >  2:323192/1‑148 (MQ=255)                                                                                                           tggtggTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACttt                                         >  5:151343/1‑147 (MQ=255)                                                                                                                 tAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGAc                                 >  7:216599/1‑149 (MQ=255)                                                                                                                      gTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCt                            >  8:61398/1‑149 (MQ=255)                                                                                                                      gTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCt                            >  2:392433/1‑149 (MQ=255)                                                                                                                             gagaATGAGCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGAt                      >  7:268151/1‑148 (MQ=255)                                                                                                                                 attaccAAACCCCGCCGATGGGCGGGCTTCAGGGGGGGGCATAATGGCTTTCGTACTACGGTCGCTTCTCGTCCACCGAAATGTAGGAATCACCCGCCCGCACTCCTCATCATGAATCTCACTTTCTGGTGACTGCCTTTGGATAAGtt                 <  7:61398/144‑1 (MQ=255)                                                                                                                                 atgccgaaaGCCCGCCGATGGGCTGGCTAGAGGGGGGGGCTGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCAACGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGtt                 <  3:369703/143‑1 (MQ=255)                                                                                                                                   ccctgaaGCCCGCCCATCGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGt               >  3:379928/6‑149 (MQ=255)                                                                                                                                     gCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCGTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTAt             >  7:99107/1‑149 (MQ=255)                                                                                                                                     gCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAg                                      >  4:244834/1‑124 (MQ=255)                                                                                                                                     ctgaaGCCCGCCCATCGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTgg                        <  3:193449/135‑1 (MQ=255)                                                                                                                                     ctgaaGCCCGCCCATCGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTgg                        >  4:193449/4‑138 (MQ=255)                                                                                                                                            ccgcccATCGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTATCCAGCCt      >  3:365467/1‑149 (MQ=255)                                                                                                                                                cgATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTATCCAGCCTGTTc  <  6:151343/149‑1 (MQ=255)                                                                                                                                                cgATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTATCCAGCCTGTTc  <  1:392433/149‑1 (MQ=255)                                                                                                                                                 |                                                                                                                                                    TGCGAATGGGCATTTTGGTCTATCCGGCGGAGAGTGAATGTCGAAGCCTGCTTCCCGGTTACGTCGGCTCCAATAAGGTGCGGGAGAGCGGTAATGATGGGGGTGATGGTGGTAAAGGTGAAAGGAGAATGAGCAAAGCCCGCCGATGGGCGGGCTTCAGGGGGGGGCAGAAGGGCTATCGTACTACGGTCGCTTCTCGTCCACCGAAAGGTAGGAAGCACCCGCCCGCACTCCTCATCAGGAATCGCACTTTCAGGTGACTGCCTTTGGATAAGTTGTATCCAGCCTGTTC  >  NC_002947/1274940‑1275231

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑