Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,949,113	T→C	15.8%	S141G (AGC→GGC)	PP_3485 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,949,113	0	T	C	15.8%	83.3 / 8.8	39	S141G (AGC→GGC)	PP_3485	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (12/20);  new base C (3/3);  total (16/23)
Fisher's exact test for biased strand distribution p-value = 6.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.76e-01

CCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCAAATGCCGCTTCGATCTCG  >  NC_002947/3948967‑3949243                                                                                                                                                    |                                                                                                                                    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                                                                                                                 <  5:69927/149‑1 (MQ=255)                  gAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGc                                                                                                                 >  3:347156/1‑149 (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)                                                                                                                                                    |                                                                                                                                    CCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCAAATGCCGCTTCGATCTCG  >  NC_002947/3948967‑3949243

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: ‑