Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A13 F1 I1 R1 778 68.7 3228504 93.4% 3015422 109.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,799,390 (T)8→7 coding (807/852 nt) waaZ ← lipopolysaccharide KdoIII transferase, lipopolysaccharide core biosynthesis protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,799,3830T.100.0% 237.1 / NA 58coding (814/852 nt)waaZlipopolysaccharide KdoIII transferase, lipopolysaccharide core biosynthesis protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (30/28);  total (30/28)

TTTCTTTTTGTGAAAAGTTCCTAAGCGCATTTTTATACCATATTATTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCATTTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCTGTATCATCTGATAAATTATAAATATTAATATCTTTTACA  >  NC_000913/3799283‑3799504
                                                                                                    |                                                                                                                         
tttcttttTGTGAAAAGTTCCTAAGCGCATTTTTATACCATATTATTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGAt                                                                                    >  1:935100/1‑139 (MQ=255)
 ttcttttTGTGAAAAGTTCCTAAGCGCATTTTTATACCATATTATTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTg                                                                                      <  2:95886/136‑1 (MQ=255)
 ttcttttTGTGAAAAGTTCCTAAGCGCATTTTTATACCATATTATTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTg                                                                                      >  1:95886/1‑136 (MQ=255)
            aaaaGTTCCTAAGCGCATTTTTATACCATATTATTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGa                                                                                                   >  2:915767/1‑112 (MQ=255)
            aaaaGTTCCTAAGCGCATTTTTATACCATATTATTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGa                                                                                                   <  1:915767/112‑1 (MQ=255)
                           cATTTTTATACCATATTATTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCa                                                                                         <  2:660837/107‑1 (MQ=255)
                           cATTTTTATACCATATTATTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCa                                                                                         >  1:660837/1‑107 (MQ=255)
                           cATTTTTATACCATATTATTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTAc                                                         >  1:694046/1‑139 (MQ=255)
                                   taCCATATTATTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCg                                                     >  2:306010/1‑135 (MQ=255)
                                   taCCATATTATTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCg                                                     <  1:306010/135‑1 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCa                                                                                                             >  2:415147/1‑74 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCa                                                                                                             <  1:415147/74‑1 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGa                                                                                                   <  1:976886/84‑1 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGa                                                                                                   >  2:976886/1‑84 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTg                                                                                           <  2:1142188/92‑1 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATaaa                                                                  <  2:1101801/117‑1 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATaaa                                                                  <  2:924096/117‑1 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATaaa                                                                  >  1:1101801/1‑117 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATaaa                                                                  >  1:924096/1‑117 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATaaa                                                                  <  2:1010195/117‑1 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATaaa                                                                  >  1:1010195/1‑117 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACa                                                        >  2:176083/1‑127 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACa                                                        <  1:176083/127‑1 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCg                                                     >  2:919448/1‑130 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCg                                                     <  1:919448/130‑1 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGaaa                                              >  1:907963/1‑137 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGaaa                                              <  2:907963/137‑1 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATa                                            >  1:116163/1‑139 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATa                                            >  2:1439976/1‑139 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATa                                            >  2:577330/1‑139 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATa                                            >  1:1219758/1‑139 (MQ=255)
                                        tattatTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTAAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTg                                                                                           >  1:1142188/1‑92 (MQ=255)
                                         attattTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAg                                           <  1:577330/139‑1 (MQ=255)
                                                     tCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCTGTATCATCTg                               >  2:1124388/1‑139 (MQ=255)
                                                       aGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGa                                                                                                   >  2:1074652/1‑69 (MQ=255)
                                                       aGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATa                                            >  2:22194/1‑124 (MQ=255)
                                                       aGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATa                                            <  1:22194/124‑1 (MQ=255)
                                                       aGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCGTGTCATATCTTTTGa                                                                                                   <  1:1074652/69‑1 (MQ=255)
                                                          atgatTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCTGTATCATCTGATaaa                          <  2:935100/139‑1 (MQ=255)
                                                            gatTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGa                                                >  1:1091853/1‑115 (MQ=255)
                                                            gatTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGa                                                <  2:1091853/115‑1 (MQ=255)
                                                               taattaGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCTGTATCATCTGATAAATtata                     <  1:394396/139‑1 (MQ=255)
                                                                aattaGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCTGTATCATCTGATAAATTATaa                    <  1:1124388/139‑1 (MQ=255)
                                                                 attaGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAg                                           <  2:441220/115‑1 (MQ=255)
                                                                 attaGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAg                                           >  1:441220/1‑115 (MQ=255)
                                                                 attaGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCt                                         <  2:508195/117‑1 (MQ=255)
                                                                 attaGCATAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCt                                         >  1:508195/1‑117 (MQ=255)
                                                                       aTAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGt                                                                          >  2:127969/1‑78 (MQ=255)
                                                                       aTAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGt                                                                          <  1:127969/78‑1 (MQ=255)
                                                                       aTAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCTGTATCATCTGATAAATTATAAATATTaa             <  2:694046/139‑1 (MQ=255)
                                                                        tAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCt                                         >  2:658953/1‑110 (MQ=255)
                                                                        tAAGAATCGGTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCt                                         <  1:658953/110‑1 (MQ=255)
                                                                                ggTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGa                                                <  2:1195676/95‑1 (MQ=255)
                                                                                ggTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGa                                                >  1:1195676/1‑95 (MQ=255)
                                                                                ggTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCTGTATCATCTGATAAATTATAAATATTAATATCTTTTa    >  2:104972/1‑139 (MQ=255)
                                                                                 gTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGt                                                                          >  2:1047808/1‑68 (MQ=255)
                                                                                 gTTGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGt                                                                          <  1:1047808/68‑1 (MQ=255)
                                                                                  ttGAAGTTCTATATTGCA‑TTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACCGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCTGTATCATCTGATAAATTATAAATATTAATATCTTTTACa  <  1:1546750/139‑1 (MQ=255)
                                                                                                    |                                                                                                                         
TTTCTTTTTGTGAAAAGTTCCTAAGCGCATTTTTATACCATATTATTTTAGTTTCAGGATGATTAATTAGCATAAGAATCGGTTGAAGTTCTATATTGCATTTTTTTTCTTGTCATATCTTTTGATTCTTCTGCACTGATGTCTTGAAGTTTAATAAATGGAATTACATCGTAAGAAATAGCTGTATCATCTGATAAATTATAAATATTAATATCTTTTACA  >  NC_000913/3799283‑3799504

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A