Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	3,517,393	T→C	D388D (GAT→GAC)	mrcA →	peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	3,517,393	0	T	C	91.1%	134.5 / 4.7	45	D388D (GAT→GAC)	mrcA	peptidoglycan glycosyltransferase/peptidoglycan DD‑transpeptidase MrcA
Reads supporting (aligned to +/- strand):  ref base T (1/3);  new base C (26/15);  total (27/18)
Fisher's exact test for biased strand distribution p-value = 2.86e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.67e-02

TGCCAACCTATGGTCCGCTGCTGCCTGCCGCAGTCACCAGCGCCAATCCTCAGCAAGCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGATACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAGTGAACTCGGCGCTGGTGTCGATCAA  >  NZ_CP009273/3517257‑3517527                                                                                                                                         |                                                                                                                                       tGCCAACCTATGGTCCGCTGCGGCCTGCTGCAGTCACCAGCGCCAATCCTCAGCAAGCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGacac                                                                                                                                      >  2:259218/1‑139 (MQ=255)   ccAACCTATGGTCCGCTGCTGCCTGCCGCAGTCACCAGCGCCAATCCTCAGCAAGCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGacac                                                                                                                                      <  1:1055677/137‑1 (MQ=255)   ccAACCTATGGTCCGCTGCTGCCTGCCGCAGTCACCAGCGCCAATCCTCAGCAAGCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGacac                                                                                                                                      <  2:1136212/137‑1 (MQ=255)                  ctgctgCCTGCCGCAGTCACCAGCGCCAATCCTCAGCAAGCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGAcgc                                                                                                                     >  2:747242/1‑139 (MQ=255)                  ctgctgCCTGCCGCAGTCACCAGCGCCAATCCTCAGCAAGCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGAcgc                                                                                                                     >  2:797133/1‑139 (MQ=255)                  ctgctgCCTGCCGCAGTCACCAGCGCCAATCCTCAGCAAGCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGAcgc                                                                                                                     >  2:502231/1‑139 (MQ=255)                           gccGCAGTCACCAGCGCCAATCCTCAGCAAGCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAg                                                                                                            >  2:183134/1‑139 (MQ=255)                                    aCCAGCGCCAATCCTCAGCAAGCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATg                                                                                                   <  1:983162/139‑1 (MQ=255)                                                     gCAAGCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAg                                                                                  <  2:384144/139‑1 (MQ=255)                                                     gCAAGCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAg                                                                                  <  2:629863/139‑1 (MQ=255)                                                         gCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCaaa                                                                              >  1:447747/1‑139 (MQ=255)                                                         gCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCaaa                                                                              >  2:1271992/1‑139 (MQ=255)                                                            aCGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCt                                                                           >  1:385361/1‑139 (MQ=255)                                                              ggCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTgg                                                                         >  1:803085/1‑139 (MQ=255)                                                               gCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTggg                                                                        <  2:385361/139‑1 (MQ=255)                                                                    gCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGATACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGt                                                                   >  2:653467/1‑139 (MQ=255)                                                                        gCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAgg                                                               >  1:1219333/1‑139 (MQ=255)                                                                            aCGTGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGGGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTgg                                                           <  2:147887/139‑1 (MQ=255)                                                                                gTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGAt                                                       >  1:563593/1‑139 (MQ=255)                                                                                     ccGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCAtg                                                  <  1:502231/139‑1 (MQ=255)                                                                                          gCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCAtg                                                  <  1:1056372/134‑1 (MQ=255)                                                                                          gCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCAtg                                                  >  2:1056372/1‑134 (MQ=255)                                                                                           cATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGATACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGtggct                                            <  2:870106/139‑1 (MQ=255)                                                                                                 gTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGcaca                                      <  1:355093/139‑1 (MQ=255)                                                                                                      gAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGATACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGc                                 <  1:195064/139‑1 (MQ=255)                                                                                                      gAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGc                                 >  1:332663/1‑139 (MQ=255)                                                                                                        aGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCg                               <  2:447747/139‑1 (MQ=255)                                                                                                          gCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCgg                              >  2:882282/1‑138 (MQ=255)                                                                                                          gCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCgg                              >  2:1131684/1‑138 (MQ=255)                                                                                                          gCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCgg                              >  1:1171919/1‑138 (MQ=255)                                                                                                          gCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCgg                              >  1:1231247/1‑138 (MQ=255)                                                                                                          gCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCgg                              >  2:556348/1‑138 (MQ=255)                                                                                                          gCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCgg                              >  2:555521/1‑138 (MQ=255)                                                                                                          gCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCgg                              >  2:457112/1‑138 (MQ=255)                                                                                                          gCGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCgg                              >  2:403366/1‑138 (MQ=255)                                                                                                           cGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCaaa                                                                                          >  2:694822/1‑77 (MQ=255)                                                                                                           cGTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCaaa                                                                                          <  1:694822/77‑1 (MQ=255)                                                                                                            gTTCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAg                           <  1:183134/139‑1 (MQ=255)                                                                                                             ttCGCTGGGCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAGt                          >  2:280459/1‑139 (MQ=255)                                                                                                                    ggCGCGTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAGTGAACt                     <  2:252336/137‑1 (MQ=255)                                                                                                                       gcgTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAGTGAACTCGgcg                <  1:556348/139‑1 (MQ=255)                                                                                                                       gcgTCCTTACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAGTGAACTCGgcg                <  2:1171919/139‑1 (MQ=255)                                                                                                                        cgTCCTTTCCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAGTGAACTCGgcgc               <  1:542500/139‑1 (MQ=255)                                                                                                                        cgTCCTTACCGTTCGGATACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAGTGAACTCGgcgc               <  1:1269808/139‑1 (MQ=255)                                                                                                                              tACCGTTCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAGTGAACTCGGCGCTGgtgt         >  2:51533/1‑139 (MQ=255)                                                                                                                                   ttCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAGTGAACTCGGCGCTGGTGTCGAt     >  2:144988/1‑138 (MQ=255)                                                                                                                                   ttCGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAGTGAACTCGGCGCTGGTGTCGAt     >  1:722764/1‑138 (MQ=255)                                                                                                                                     cGGACACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAGTGAACTCGGCGCTGGTGTCGATCaa  >  2:1586/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                       TGCCAACCTATGGTCCGCTGCTGCCTGCCGCAGTCACCAGCGCCAATCCTCAGCAAGCGACGGCGATGCTGGCGGACGGGTCGACCGTCGCATTGAGTATGGAAGGCGTTCGCTGGGCGCGTCCTTACCGTTCGGATACTCAGCAAGGACCGACGCCGCGTAAAGTGACCGATGTTCTGCAAACGGGTCAGCAAATCTGGGTTCGTCAGGTTGGCGATGCATGGTGGCTGGCACAAGTGCCGGAAGTGAACTCGGCGCTGGTGTCGATCAA  >  NZ_CP009273/3517257‑3517527

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑