Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	573,559	G→T	8.4%	S108S (TCG→TCT)	PP_0487 →	membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	573,559	0	G	T	8.4%	133.9 / 2.1	46	S108S (TCG→TCT)	PP_0487	membrane protein
Reads supporting (aligned to +/- strand):  ref base G (23/19);  new base T (2/2);  total (25/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.40e-01

GGCCAGGAAAAACTGGTCAGTACCCTCGGCACGCTGGCGGCTATCCGCAACTTCCTGGCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTCGAGGAGCGCGAACTGTCATCGCGCATGCTGTTCACCGTGGTCCCGCTGACCT  >  NC_002947/573413‑573698                                                                                                                                                   |                                                                                                                                            ggCCAGGAAAAACTGGTCAGTACCCTCGGCACGCTGGCGGCTATCCGCAACTTCCTGGCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGa                                                                                                                                            <  3:11856/148‑1 (MQ=255)      ggAAAAACTGGTCAGTACCCTCGGCACGCTGGCGGCTATCCGCAACTTCCTGGCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCg                                                                                                                                       >  4:134020/1‑148 (MQ=255)            ccTGGTCAGTACCCTCGGCACGCTGGCGGCTATCCGCAACTTCCTGGCCAAGAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGaaa                                                                                                                                <  5:167276/148‑1 (MQ=255)                       cccTCGGCACGCTGGCGGCTATCCGCAACTTCCTGGCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCa                                                                                                                       >  1:237371/1‑147 (MQ=255)                       cccTCGGCACGCTGGCGGCTATCCGCAACTTCCTGGCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCa                                                                                                                       <  2:237371/147‑1 (MQ=255)                        ccTCGGCACGCTGGCGGCTATCCGCAACTTCCTGGCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGc                                                                                                                        >  1:73451/1‑145 (MQ=255)                          tCGGCACTCTGGCGGCTATCCGCAACTTCCTGGCCAACTGCAAGATTGTCTGGCATGTAGCGTTGGGCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTGGCAGGAAACTGTGGGCAAGatc                                                                                                                  <  4:254625/149‑1 (MQ=255)                                         cTATCCGCAACTTCCTGGCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATc                                                                                                   <  8:231318/149‑1 (MQ=255)                                          tATCCGCAACTTCCTGGCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATcc                                                                                                  >  3:18765/1‑149 (MQ=255)                                              cGCAACTTCCTGGCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCt                                                                                              <  4:18765/149‑1 (MQ=255)                                              cGCAACTTCCTGGCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCAGCt                                                                                              >  2:68751/1‑149 (MQ=255)                                               gCAACTTCCTGGCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGTGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATAGTGTCGATATCGCATGAAACTGTCTGCAACATAATCCTGGCACTGATCACGc                                                                                               >  3:66503/1‑147 (MQ=255)                                                        tcgCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATtct                                                                                     >  6:221512/3‑148 (MQ=255)                                                          gCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCa                                                                                   <  5:221512/148‑1 (MQ=255)                                                                  cAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCtt                                                                           >  2:216004/1‑148 (MQ=255)                                                                  cAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTa                                                                          <  1:216004/149‑1 (MQ=255)                                                                  cAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTa                                                                          >  3:350284/1‑149 (MQ=255)                                                                         gTCTTGCATGTAGCGGTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGACTACCTGGGGGCTCACCTTATCGTCTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCTCTCGGTATTCTCATTTTCCTTACCCGCa                                                                    <  8:306665/148‑1 (MQ=255)                                                                          tCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTc                                                                              <  3:143070/137‑1 (MQ=255)                                                                          tCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTc                                                                              >  4:143070/1‑137 (MQ=255)                                                                            tGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAg                                                                  <  2:319828/147‑1 (MQ=255)                                                                            tGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAg                                                                  >  1:319828/1‑147 (MQ=255)                                                                                    aGCTTTGGTCGTGGTGCCTTTTTAGCTGCTAGGGGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCg                                                         <  4:66503/148‑1 (MQ=255)                                                                                       gTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTc                                                      >  3:81826/1‑148 (MQ=255)                                                                                          ggTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTCCCCCCAAGGACCGCCCGGTCgag                                                   <  6:80449/148‑1 (MQ=255)                                                                                          ggTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTCgag                                                   <  6:220351/148‑1 (MQ=255)                                                                                           gTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGt                                                       <  3:312274/143‑1 (MQ=255)                                                                                           gTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGt                                                       >  4:312274/1‑143 (MQ=255)                                                                                                    ccGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTCGAGGAGCGCGAACt                                        <  4:81826/149‑1 (MQ=255)                                                                                                            gctgctAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTCga                                                    <  2:309403/129‑1 (MQ=255)                                                                                                            gctgctAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTCga                                                    >  1:309403/1‑129 (MQ=255)                                                                                                                ctAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTAgcc                                                                       <  2:266549/106‑1 (MQ=255)                                                                                                                ctAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTAccc                                                                       >  1:266549/1‑106 (MQ=255)                                                                                                                   ggCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCTGCTCGGTATTCTCATTTTCCTTACCCCCGCGGACCGCCCGGTCGAGGAGCGCGAACTGTCATCGCGCATGCt                         <  1:68751/149‑1 (MQ=255)                                                                                                                    gcgcCTACCTGGGGGCTCACCTGATCGTGTCTATCTCg                                                                                                                                       <  7:270967/38‑1 (MQ=255)                                                                                                                    gcgcCTACCTGGGGGCTCACCTGATCGTGTCTATCTCg                                                                                                                                       <  7:275862/38‑1 (MQ=255)                                                                                                                    gcgcCTACCTGGGGGCTCACCTGATCGTGTCTATCTCg                                                                                                                                       >  8:270967/1‑38 (MQ=255)                                                                                                                    gcgcCTACCTGGGGGCTCACCTGATCGTGTCTATCTCg                                                                                                                                       >  8:275862/1‑38 (MQ=255)                                                                                                                      gcCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTCGAGGAGCGCGAACTGTCATCGCGCATGCTGtt                      >  7:111319/1‑149 (MQ=255)                                                                                                                         tACCTGGGGGCTCACCTGATCGTGTAGATCTCGCAGGAAACTGTGTGCAATATAATAATGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTCGAGGAGCGCGAACTGTCATCGCGCATGCTGTTCAc                   >  2:11163/1‑149 (MQ=255)                                                                                                                         tACCTGGGCTCTCACCTGATCGTGTCGATCTCGAAGGAAACTGTGGGCAAGATCATCCTGGCAATGATCCCTAACGGTATTATCATTTACCTTACCCCCAAGCACCGCCCCGTCGAGGAGCGCGAACTCTCATCGCGCATGCTGATCAc                   >  2:232271/1‑149 (MQ=255)                                                                                                                            cTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTCGAGGAGCGCGAACTGTCATCGCGCATGCTGTTCACCGt                >  1:358427/1‑149 (MQ=255)                                                                                                                               ggggCTCACCTGATCGTGTCGATCTCGAAGGAAACTGTGGGCAAGATAATCATGGAAATGATCAAGCTCGGTATTATCATTTTCCATAACCACAAGGACAGCCCGGTCGAGGACCGCGTCCTCTCATCGCCGATCCTGTACAACGTGGt             >  8:249081/1‑149 (MQ=255)                                                                                                                                 ggCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTCGAGGAGCGCGAACTGTCATCGCGCATGCTGTTCACCGTGGTcc           >  2:102280/1‑149 (MQ=255)                                                                                                                                    tCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTCGAGGAGCGCGAACTGTCATCGCGCATGCTGTTCACCGTGGTCCCGc        >  6:56754/1‑149 (MQ=255)                                                                                                                                          gATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTCGAGGAGCGCGAACTGTCATCGCGCATGCTGTTCACCGTGGTCCCGCTGAcct  >  4:225842/1‑149 (MQ=255)                                                                                                                                                   |                                                                                                                                            GGCCAGGAAAAACTGGTCAGTACCCTCGGCACGCTGGCGGCTATCCGCAACTTCCTGGCCAACAGCAAGATGGTCTGGCAGGTAGCGTTGGTCGGGGTGCCGTTTTCGCTGCTAGGCGCCTACCTGGGGGCTCACCTGATCGTGTCGATCTCGCAGGAAACTGTGGGCAAGATCATCCTGGCACTGATCCCGCTCGGTATTCTCATTTTCCTTACCCCCAAGGACCGCCCGGTCGAGGAGCGCGAACTGTCATCGCGCATGCTGTTCACCGTGGTCCCGCTGACCT  >  NC_002947/573413‑573698

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: ‑