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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,560,390 A→G 25.9% N133D (AAT→GAT)  evgS → hybrid sensory histidine kinase in two‑component regulatory system with EvgA

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,560,3900AG25.9% 88.4 / 28.3 77N133D (AAT→GAT) evgShybrid sensory histidine kinase in two‑component regulatory system with EvgA
Reads supporting (aligned to +/- strand):  ref base A (30/27);  new base G (6/14);  total (36/41)
Fisher's exact test for biased strand distribution p-value = 1.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.58e-01

GACGCGCTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTC  >  minE/1560324‑1560457
                                                                  |                                                                   
gACGCGCTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTaataat                                                                   >  1:3431606/1‑69 (MQ=255)
gACGCGCTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTaataat                                                                   >  1:1926327/1‑69 (MQ=255)
gACGCGCTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTaataat                                                                   >  1:656430/1‑69 (MQ=255)
gACGCGCTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTaataat                                                                   >  1:821862/1‑69 (MQ=255)
gACGCGCTTGCAGAAGGTGAAGTCGATATAGTGTTATAACATTTAGTTACTTCGCCGCCTCTTaataat                                                                   >  1:1801110/1‑69 (MQ=255)
   gcgcTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGAc                                                                <  1:2742056/69‑1 (MQ=255)
   gcgcTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGAc                                                                <  1:1119634/69‑1 (MQ=255)
   gcgcTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGAc                                                                <  1:3078097/69‑1 (MQ=255)
   gcgcTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGAc                                                                <  1:684014/69‑1 (MQ=255)
   gcgcTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGAc                                                                <  1:1049765/69‑1 (MQ=255)
    cgcTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGAc                                                                <  1:788270/68‑1 (MQ=255)
    cgcTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGAc                                                                <  1:1968406/68‑1 (MQ=255)
                   aaGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCaaccaaac                                                <  1:3019047/69‑1 (MQ=255)
                   aaGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCaaccaaac                                                <  1:2706697/69‑1 (MQ=255)
                   aaGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCaaccaaac                                                <  1:2036661/69‑1 (MQ=255)
                     gTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCaaccaaacca                                              <  1:547996/69‑1 (MQ=255)
                     gTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCaaccaaacca                                              <  1:2194420/69‑1 (MQ=255)
                     gTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCaaccaaac                                                <  1:2566511/67‑1 (MQ=255)
                        gATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCAtt                                            >  1:1066472/1‑68 (MQ=255)
                        gATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTg                                           <  1:3232335/69‑1 (MQ=255)
                        gATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTg                                           <  1:3428047/69‑1 (MQ=255)
                        gATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTg                                           <  1:2856705/69‑1 (MQ=255)
                        gATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTg                                           <  1:692491/69‑1 (MQ=255)
                        gATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTg                                           <  1:786171/69‑1 (MQ=255)
                         atatAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTg                                           <  1:2436847/68‑1 (MQ=255)
                          tataGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGAt                                         <  1:1707980/69‑1 (MQ=255)
                          tataGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGAt                                         <  1:33207/69‑1 (MQ=255)
                          tataGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGAt                                         <  1:2963419/69‑1 (MQ=255)
                          tataGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGAt                                         <  1:541466/69‑1 (MQ=255)
                          tataGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGAt                                         <  1:2685064/69‑1 (MQ=255)
                              gtgtTATCACATTTAGTTACTTCGCCGCCTCTtaataa                                                                    >  1:2584668/1‑38 (MQ=255)
                              gtgtTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAAtt                                     >  1:2898276/1‑69 (MQ=255)
                                 ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                  >  1:1600036/1‑69 (MQ=255)
                                 ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                  >  1:3196637/1‑69 (MQ=255)
                                 ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                  >  1:1715403/1‑69 (MQ=255)
                                 ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                  >  1:777748/1‑69 (MQ=255)
                                 ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                  >  1:1229893/1‑69 (MQ=255)
                                 ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                  >  1:2472257/1‑69 (MQ=255)
                                 ttATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTAcc                                  >  1:2271895/1‑69 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATTACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:1451483/69‑1 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTTATAATTACCTTTCCgg                           <  1:1362709/69‑1 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:3284385/69‑1 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:1690143/69‑1 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:812807/69‑1 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:1404590/69‑1 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:2014876/69‑1 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:1895882/69‑1 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:1084148/69‑1 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:2893105/69‑1 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:2406511/69‑1 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:527599/69‑1 (MQ=255)
                                        aTTTAGTTGCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:776585/69‑1 (MQ=255)
                                        aTTTAGTTCCTTCGCCGCCTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAATTACCTTTCCgg                           <  1:623250/69‑1 (MQ=255)
                                                aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCtt                                >  1:1410282/1‑56 (MQ=255)
                                                aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                   >  1:1197372/1‑69 (MQ=255)
                                                aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                   >  1:3036438/1‑69 (MQ=255)
                                                aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                   >  1:2943834/1‑69 (MQ=255)
                                                aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                   >  1:3113352/1‑69 (MQ=255)
                                                aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                   >  1:195247/1‑69 (MQ=255)
                                                aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                   >  1:1560251/1‑69 (MQ=255)
                                                aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                   >  1:2573017/1‑69 (MQ=255)
                                                aCTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTa                   >  1:1415699/1‑69 (MQ=255)
                                                   tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                >  1:760449/1‑69 (MQ=255)
                                                   tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                >  1:382197/1‑69 (MQ=255)
                                                   tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                >  1:846277/1‑69 (MQ=255)
                                                   tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                >  1:2308821/1‑69 (MQ=255)
                                                   tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                >  1:2464606/1‑69 (MQ=255)
                                                   tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                >  1:2724846/1‑69 (MQ=255)
                                                   tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                >  1:3079193/1‑69 (MQ=255)
                                                   tCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacc                >  1:3059634/1‑69 (MQ=255)
                                                      ccgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacca               <  1:2117696/67‑1 (MQ=255)
                                                      ccgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacca               <  1:3139262/67‑1 (MQ=255)
                                                       cgccTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAAt                                      >  1:1071745/1‑43 (MQ=19)
                                                       cgccTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAAt                                      >  1:276565/1‑43 (MQ=19)
                                                       cgccTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAAt                                      >  1:384140/1‑43 (MQ=19)
                                                       cgccTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAAt                                      >  1:358164/1‑43 (MQ=19)
                                                       cgccTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAAt                                      >  1:3091974/1‑43 (MQ=19)
                                                       cgccTCTTAATGATGACATTGCTGCAACTAATCCTCTGATAAt                                      >  1:405501/1‑43 (MQ=19)
                                                       cgccTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAacca               <  1:449320/66‑1 (MQ=255)
                                                           tctTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTc         >  1:1243945/1‑68 (MQ=255)
                                                           tctTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTc         >  1:143559/1‑68 (MQ=255)
                                                           tctTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTc         >  1:1551237/1‑68 (MQ=255)
                                                           tctTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTc         >  1:1919997/1‑68 (MQ=255)
                                                                  aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc  <  1:3193163/68‑1 (MQ=255)
                                                                  aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc  <  1:1417385/68‑1 (MQ=255)
                                                                  aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc  <  1:1610961/68‑1 (MQ=255)
                                                                  aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc  <  1:2015156/68‑1 (MQ=255)
                                                                  aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc  <  1:3177761/68‑1 (MQ=255)
                                                                  aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc  <  1:3170854/68‑1 (MQ=255)
                                                                  aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc  <  1:3161870/68‑1 (MQ=255)
                                                                  aatGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTc  <  1:2483642/68‑1 (MQ=255)
                                                                  |                                                                   
GACGCGCTTGCAGAAGGTGAAGTCGATATAGTGTTATCACATTTAGTTACTTCGCCGCCTCTTAATAATGACATTGCTGCAACCAAACCATTGATAATTACCTTTCCGGCGCTGGTAACCACCCTTCACGACTC  >  minE/1560324‑1560457

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A