Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,949,097	G→A	11.9%	P146L (CCG→CTG)	PP_3485 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,949,097	0	G	A	11.9%	106.5 / 4.8	45	P146L (CCG→CTG)	PP_3485	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (17/20);  new base A (2/3);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCGCCTGCGCCTCCCGCTGCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCAAATGCCGCTTCGATCTCG  >  NC_002947/3948948‑3949243                                                                                                                                                      |                                                                                                                                                     gcgcctgcgcctCCCGCTGCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATC‑AAAAATGCCTCCACTTCGCCctcgctcg                                                                                                                                                      >  1:370079/1‑149 (MQ=255)    cctgcgcctCCCGCTGCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGgc                                                                                                                                                    >  4:310699/1‑149 (MQ=255)        cgcctCCCGCTGCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGgcgc                                                                                                                                                  <  3:80769/147‑1 (MQ=255)         gcctCCCGCTGCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTc                                                                                                                                              >  6:302960/1‑149 (MQ=255)              ccGCTGCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTg                                                                                                                                         >  5:337448/1‑149 (MQ=255)              ccGCTGCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTg                                                                                                                                         >  3:34808/1‑149 (MQ=255)                    cccGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCt                                                                                                                                     <  5:9555/147‑1 (MQ=255)                    cccGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCt                                                                                                                                     >  3:231692/1‑147 (MQ=255)                    cccGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGa                                                                                                                                   <  7:90769/149‑1 (MQ=255)                      cGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATCGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGc                                                                                                                                 <  8:251704/149‑1 (MQ=255)                        aTGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑Ag                                                                                                                              <  6:8425/149‑1 (MQ=255)                          gcgCGGTGCACGAGCCACGGCCAGGCCGTGTTCGCGTATGCCCAATGGATTATCACTTTGGTTCTGAGCGCCTTGCAGTCTGTCCTGGTTTGCATCAAAAACTGCCTCCACTTCGCCAT‑GCTCAGCGCAGTCGAC‑GCGCCGAGcgagg                                                                                                                             <  8:269319/146‑5 (MQ=255)                                  cccGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCT‑GCTCAGCGCAGTCGAC‑GCGCCGAGcgagg                                                                                                                             <  5:27266/140‑5 (MQ=38)                                  cccGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCT‑GCTCAGCGCAGTCGAC‑GCGCCGAGcgagg                                                                                                                             >  6:27266/1‑136 (MQ=38)                                     gAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGc                                                                                                                 >  3:347156/1‑149 (MQ=255)                                     gAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGc                                                                                                                 <  5:69927/149‑1 (MQ=255)                                        ccAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTgg                                                                                                              <  4:231692/149‑1 (MQ=255)                                             gccaggccGTGTTCGTGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCCGCGCAGTCGAC‑GCGCCGAGCGAGGGCgaagtgga                                                                                                                   >  2:353345/1‑133 (MQ=37)                                             gccaggccGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCAGCGCAGTCGAC‑GCGCCGAGCGAGGGCgaagtgga                                                                                                                   <  1:353345/140‑8 (MQ=37)                                             gccaggccGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATC‑AAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGgccgcc                                                                                                        <  2:370079/149‑1 (MQ=255)                                                   ccttcttCGCCTATTCCCAATGGAATATCACTTTGGTTCTCCGCTCCTTGCATTCTGTCCAGGTTGTCATCAAAAAATGCCTCCACTTCGCCCTCTCTCCGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCAtctc                                                                                                   <  8:347179/144‑1 (MQ=255)                                                    cGTGTTCGCGTATGACCAATGGATTATCACTTTGTTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTAGACTGCGCAGAGC‑AGGGCCTACACTTGCTGGGCCGCAAtctc                                                                                                   >  1:182116/1‑148 (MQ=255)                                                     gtgtTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCAt                                                                                                 >  1:128413/1‑149 (MQ=255)                                                      tgtTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATg                                                                                                <  2:292857/149‑1 (MQ=255)                                                            cgTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGgt                                                                                          <  5:302960/149‑1 (MQ=255)                                                                 gACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTAt                                                                                      >  4:169488/1‑148 (MQ=255)                                                                    cactGGATTATCACTATGGATCTGCGCTCCTAGCCGTCTGTCCTCGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAg                                                                                  <  6:288869/146‑1 (MQ=255)                                                                     aaTGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCACTCGCTCTGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAgt                                                                                 >  1:364675/1‑149 (MQ=255)                                                                                    tGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTc                                                                  >  3:272598/1‑149 (MQ=255)                                                                                       ttCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTc                                                                  <  4:254425/146‑1 (MQ=255)                                                                                       ttCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTc                                                                  >  3:254425/1‑146 (MQ=255)                                                                                            cgcTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGc                                                             <  4:347156/146‑1 (MQ=255)                                                                                             gcTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCAACTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGc                                                         >  4:356617/1‑149 (MQ=255)                                                                                                 cTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCctct                                                     >  4:378865/1‑149 (MQ=255)                                                                                                  ttGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTg                                                    >  3:69143/1‑149 (MQ=255)                                                                                                    gCAGTCTGTCCTGGTTGGCATCAAAAAATGCCGCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTg                                                    <  4:139977/147‑1 (MQ=255)                                                                                                      aGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTAtt                                                                                     >  3:185157/1‑112 (MQ=255)                                                                                                      aGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTAtt                                                                                     <  4:185157/112‑1 (MQ=255)                                                                                                        tCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTc                                              <  6:337448/149‑1 (MQ=255)                                                                                                                 gTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTc                                       <  4:34808/147‑1 (MQ=255)                                                                                                                 gTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCg                                      <  4:272598/148‑1 (MQ=255)                                                                                                                         cAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCGCGCCTCTGCCAGTCGCCTTTCGAATAACGcc                             >  4:226252/1‑149 (MQ=255)                                                                                                                                tGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGc                      <  4:367531/149‑1 (MQ=255)                                                                                                                                    tCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCaaa                  >  1:12688/1‑149 (MQ=255)                                                                                                                                        gtacGCCCT‑GCTCAGCGCAGTCGAC‑GCGCCGAGCGAGGGCGTACACTTGCTGGGCCGCGATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCAAATGcc              >  8:82219/4‑149 (MQ=37)                                                                                                                                             cccTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCAAATGCCGCTTc         <  7:130637/149‑1 (MQ=255)                                                                                                                                                      ggCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCAAATGCCGCTTCGATCTCg  <  3:169488/147‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                                     GCGCCTGCGCCTCCCGCTGCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCAAATGCCGCTTCGATCTCG  >  NC_002947/3948948‑3949243

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑