Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	54,743	T→C	intergenic (‑41/+12)	surA ← / ← lptD	peptidyl‑prolyl cis‑trans isomerase SurA/lipopolysaccharide assembly protein LptD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	54,743	0	T	C	100.0%	104.5 / NA	30	intergenic (‑41/+12)	surA/lptD	peptidyl‑prolyl cis‑trans isomerase SurA/lipopolysaccharide assembly protein LptD
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (11/19);  total (11/19)

GCGATACCGAGAAGCAGCGTTTTCCAGTTCTTCATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGTAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCTTGCGTACCCAGACCGTAGTT  >  NC_000913/54668‑54820                                                                            |                                                                              gCGATACCGAGAAGCAGCGTTTTCCAGTTCTTCATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAAt                                                                           <  2:11039/80‑1 (MQ=255) gCGATACCGAGAAGCAGCGTTTTCCAGTTCTTCATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATc                                                                          <  1:11040/81‑1 (MQ=255)  cGATACCGAGAAGCAGCGTTTTCCAGTTCTTCATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATca                                                                         <  2:11041/81‑1 (MQ=255)     tACCGAGAAGCAGCGTTTTCCAGTTCTTCATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATcaaca                                                                      <  1:11042/81‑1 (MQ=255)        cGAGAAGCAGCGTTTTCCAGTTCTTCATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATCAACAAAt                                                                   <  2:11045/81‑1 (MQ=255)        cGAGAAGCAGCGTTTTCCAGTTCTTCATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATCAACAAAt                                                                   <  2:11043/81‑1 (MQ=255)         gagaAGCAGCGTTTTCCAGTTCTTCATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATCAACAAATc                                                                  <  1:11046/81‑1 (MQ=255)           gaAGCAGCGTTTTCCAGTTCTTCATACTTTGTCCATTTCAATTAACCGCACTGCGGATTACGTGGCGAATCAACAAATcac                                                                <  1:11047/81‑1 (MQ=255)                    ttttCCAGTTCTTCATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGttt                                                       >  2:11092/1‑81 (MQ=255)                           gTTCTTCATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACg                                                <  1:11048/81‑1 (MQ=255)                              cttcATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACgg                                               >  2:11089/1‑79 (MQ=255)                                 cATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGaa                                          >  2:11083/1‑81 (MQ=255)                                  aTACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAAt                                         >  2:11090/1‑81 (MQ=255)                                     cTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGtt                                      <  2:11049/81‑1 (MQ=255)                                       ttttCCATTTCAATTAACCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTc                                     >  1:11093/1‑80 (MQ=255)                                            cATTTCAATTAACCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACg                                <  1:11050/80‑1 (MQ=255)                                              tttCAATTAACCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACgcag                             <  2:11051/81‑1 (MQ=255)                                                    ttAACCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCAtctc                       <  2:11052/81‑1 (MQ=255)                                                    ttAACCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCAtctc                       <  2:11053/81‑1 (MQ=255)                                                      aaCCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCtt                     >  2:11112/1‑81 (MQ=255)                                                       aCCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCtt                     <  2:11054/80‑1 (MQ=255)                                                       aCCGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCTTg                    >  1:11085/1‑81 (MQ=255)                                                        ccGCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCTTGc                   <  1:11055/81‑1 (MQ=255)                                                          gCACTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCTTGCGt                 <  1:11056/81‑1 (MQ=255)                                                            aCTGCGGATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCTTGCGTAc               >  2:11086/1‑81 (MQ=255)                                                                  gATTACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCTTGCGTACCCAGAc         >  2:11106/1‑81 (MQ=255)                                                                     tACGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCTTGCGTACCCAGACCg       >  2:11100/1‑80 (MQ=255)                                                                      aCGTGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCTTGCGTACCCAGACCGt      <  1:11057/80‑1 (MQ=255)                                                                         tGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCTTGCGTACCCAGACCGTAGtt  >  2:11088/1‑81 (MQ=255)                                                                         tGGCAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCTTGCGTACCCAGACCGTAGtt  <  1:11058/81‑1 (MQ=255)                                                                            |                                                                              GCGATACCGAGAAGCAGCGTTTTCCAGTTCTTCATACTTTTTCCATTTCAATTAACCGCACTGCGGATTACGTGGTAAATCAACAAATCACAAAGTGTTTTGATACGGCAGAATGTTCGAACGCAGCATCTCTTGCGTACCCAGACCGTAGTT  >  NC_000913/54668‑54820

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑