Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,949,097	G→A	10.4%	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	10.4%	124.9 / 4.5	48	P146L (CCG→CTG)	PP_3485	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (22/21);  new base A (2/3);  total (24/24)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.19e-01

CTGCGCCTCCCGCTGCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCAAATGCCGCTTC  >  NC_002947/3948952‑3949236                                                                                                                                                  |                                                                                                                                              ctgcgcctCCCGCTGCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGgcg                                                                                                                                            >  6:54592/1‑149 (MQ=255)    cgcctCCCGCTGCCCGATGAGCGTTGCCCGAGCTAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGgcgc                                                                                                                                           <  6:25138/147‑1 (MQ=255)        tCCCGCTGCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGAc                                                                                                                                    >  2:223445/1‑149 (MQ=255)          ccGCTGCCCGAGGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACt                                                                                                                                   <  8:181099/148‑1 (MQ=255)               gCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCt                                                                                                                              >  8:243695/1‑148 (MQ=255)                  cGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCT‑GCTCAGCGCAGTCGAC‑GCGCCGAGc                                                                                                                          >  3:1406/1‑148 (MQ=255)                   gATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAg                                                                                                                           >  8:226224/1‑147 (MQ=255)                       aGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGc                                                                                                                    <  3:87067/149‑1 (MQ=255)                       aGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCT‑GCTCAGCGCAGTCGAC‑GCGCCGAGcgaggg                                                                                                                     <  8:2356/148‑6 (MQ=38)                         cGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCg                                                                                                                   >  8:298388/1‑148 (MQ=255)                           ttGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑Gt                                                                                                                                        <  1:315451/126‑1 (MQ=255)                           ttGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑Gt                                                                                                                                        >  2:315451/1‑126 (MQ=255)                              cccGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCT‑GCTCAGCGCAGTCGAC‑GCGCCGAGCGAGGGCgaagtg                                                                                                              <  4:1406/148‑6 (MQ=37)                               ccGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACtt                                                                                                            >  5:58179/1‑149 (MQ=255)                                 gAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGc                                                                                                          >  2:183636/1‑149 (MQ=255)                                     cAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGGATCAAAAAATGCCTCCACTTCGCCCT‑GCTCAGCGCAGTCGAC‑GCGCCGAGcgaggg                                                                                                                     >  1:105789/1‑129 (MQ=37)                                     cAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCT‑GCTCAGCGCAGTCGAC‑GCGCCGAGcgaggg                                                                                                                     <  2:105789/134‑6 (MQ=37)                                               ccGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCAtctc                                                                                            <  7:298388/149‑1 (MQ=255)                                                   gtTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGc                                                                                        >  5:253686/1‑149 (MQ=255)                                                       gcgTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCggg                                                                                    <  7:226224/149‑1 (MQ=255)                                                            tGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTAt                                                                               >  7:228340/1‑149 (MQ=255)                                                               ccAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCa                                                                            <  8:34658/149‑1 (MQ=255)                                                               ccAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCa                                                                            <  6:58179/149‑1 (MQ=255)                                                                cAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTggg                                                                                                      <  6:158642/122‑1 (MQ=255)                                                                cAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTggg                                                                                                      >  5:158642/1‑122 (MQ=255)                                                                          tCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGc                                                                                                          <  8:114579/108‑1 (MQ=255)                                                                          tCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGc                                                                                                          >  7:114579/1‑108 (MQ=255)                                                                            aCTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGcc                                                                <  1:223445/148‑1 (MQ=255)                                                                              tttGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTg                                                             >  3:137853/1‑149 (MQ=255)                                                                                   ttCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTgc                                                                   >  7:173974/1‑138 (MQ=255)                                                                                   ttCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTgc                                                                   <  8:173974/138‑1 (MQ=255)                                                                                   ttCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCg                                                          >  1:72093/1‑147 (MQ=255)                                                                                   ttCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGaa                                                        <  2:72093/149‑1 (MQ=255)                                                                                   ttCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGaa                                                        <  8:228340/149‑1 (MQ=255)                                                                                      tGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGcc                                                     >  2:20090/1‑149 (MQ=255)                                                                                         gcTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCAt                                                                                          >  7:200404/1‑109 (MQ=255)                                                                                         gcTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCAt                                                                                          <  8:200404/109‑1 (MQ=255)                                                                                         gcTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGc                                                  >  7:236496/1‑149 (MQ=255)                                                                                              ttGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTg                                             >  6:103240/1‑149 (MQ=255)                                                                                                    tCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGGCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTc                                       <  6:253686/149‑1 (MQ=255)                                                                                                             gTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTc                                <  5:54592/147‑1 (MQ=255)                                                                                                                   aTCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGCTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACg                        >  8:36522/1‑149 (MQ=255)                                                                                                                          aaTGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCt                 <  1:183636/149‑1 (MQ=255)                                                                                                                                tCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCaaa           >  3:247751/1‑149 (MQ=255)                                                                                                                                  cACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCAAAt          <  7:36522/148‑1 (MQ=255)                                                                                                                                         ccccCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCAAATGCCGCTTc  <  8:49821/149‑1 (MQ=255)                                                                                                                                         cccTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGa                              <  6:306068/121‑1 (MQ=255)                                                                                                                                         cccTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGa                              >  5:306068/1‑121 (MQ=255)                                                                                                                                                  |                                                                                                                                              CTGCGCCTCCCGCTGCCCGATGAGCGTTGCCCGAGCCAAGGCCAGGCCGTGTTCGCGTATGACCAATGGATTATCACTTTGGTTCTGCGCTCCTTGCAGTCTGTCCTGGTTGGCATCAAAAAATGCCTCCACTTCGCCCTCGCTCGGCGC‑GTCGACTGCGCTGAGC‑AGGGCGTACACTTGCTGGGCCGCCATCTCATGCCGGGTGTATTCAGTGTACTGCGCCCTGTCGAAGCCCGCCTCTGCCAGTCGCCTTTCGAATAACGCCGGGCTGCCAAATGCCGCTTC  >  NC_002947/3948952‑3949236

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑