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
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 527,659 A→G 44.1% K163E (AAA→GAA)  ylbH → conserved hypothetical protein, rhs‑like

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb527,6590AG44.1% 19.3 / 92.9 68K163E (AAA→GAA) ylbHconserved hypothetical protein, rhs‑like
Reads supporting (aligned to +/- strand):  ref base A (18/20);  new base G (12/18);  total (30/38)
Fisher's exact test for biased strand distribution p-value = 6.26e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CATTTTGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTAAAGCTATCCCATTCTGA  >  W3110S.gb/527591‑527729
                                                                    |                                                                      
cATTTTGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGaaa                                                                        >  1:3356650/1‑69 (MQ=255)
  ttttGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAaga                                                                    <  1:662144/71‑1 (MQ=255)
    ttGTCGAGTTTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGaaaaa                                                                      >  1:3044023/1‑67 (MQ=255)
    ttGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGaaaaa                                                                      >  1:2563174/1‑67 (MQ=255)
      gTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAagagat                                                                 <  1:4573586/70‑1 (MQ=255)
       tCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAagagatta                                                               <  1:2600026/71‑1 (MQ=255)
         gAGTGTCTAAATTAAATGACGCGGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAagagattag                                                              <  1:4047489/70‑1 (MQ=255)
            tgtCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAagagattagagat                                                          <  1:1705352/71‑1 (MQ=255)
             gtCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAagagattagagat                                                          <  1:2910445/70‑1 (MQ=255)
              tCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATgaagaa                                                                      <  1:139861/57‑1 (MQ=255)
               cTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAagagat                                                                 >  1:3176522/1‑61 (MQ=255)
                taaattaaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGaaaa                                                                       <  1:2753458/54‑1 (MQ=255)
                taaattaaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGaaaa                                                                       <  1:153585/54‑1 (MQ=255)
                taaattaaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTACg                                                      >  1:4299313/1‑71 (MQ=255)
                taaattaaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAaga                                                                    >  1:2019308/1‑57 (MQ=255)
                 aaattaaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAagagattagagat                                                          <  1:3687204/66‑1 (MQ=255)
                 aaattaaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACgg                                                     >  1:1303465/1‑71 (MQ=255)
                  aattaaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAagagatt                                                                >  1:1333741/1‑59 (MQ=255)
                   attaaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACggg                                                    <  1:1613918/70‑1 (MQ=255)
                    ttaaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGtt                                                  <  1:2870717/71‑1 (MQ=255)
                    ttaaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGtt                                                  <  1:765991/71‑1 (MQ=255)
                     taaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGtt                                                  >  1:3509620/1‑70 (MQ=255)
                      aaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAagagat                                                                 <  1:3995641/54‑1 (MQ=255)
                      aaatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAagagat                                                                 <  1:1222311/54‑1 (MQ=255)
                       aatGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAagagattagagat                                                          <  1:2336206/60‑1 (MQ=255)
                       aatGACGCTGGTGTTAGCCGATCGGCGAAAGCGCTGGGTTATGAAAAagagattagagat                                                          <  1:4017849/60‑1 (MQ=255)
                         tGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATc                                             <  1:153163/71‑1 (MQ=255)
                           aCGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTg                                           <  1:2958293/71‑1 (MQ=255)
                              cTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAagagatta                                                               <  1:1069880/48‑1 (MQ=255)
                              cTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTc                                        <  1:1758333/71‑1 (MQ=255)
                                ggTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAagagatta                                                               >  1:889510/1‑46 (MQ=255)
                                ggTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCgg                                      >  1:251996/1‑71 (MQ=255)
                                ggTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCgg                                      >  1:645139/1‑71 (MQ=255)
                                 gtgtTAGCCGATCGGCGAAAGGGCTGGGTTGTGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGt                                     <  1:2417360/71‑1 (MQ=255)
                                 gtgtTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCgg                                      <  1:2899377/70‑1 (MQ=255)
                                 gtgtTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCgg                                      <  1:2681247/70‑1 (MQ=255)
                                 gtgtTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCgg                                      <  1:2218265/70‑1 (MQ=255)
                                 gtgtTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGt                                     <  1:2361271/71‑1 (MQ=255)
                                 gtgtTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGt                                     <  1:91338/71‑1 (MQ=255)
                                  tgtTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTAc                                                       <  1:2549583/52‑1 (MQ=255)
                                  tgtTAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTAc                                                       <  1:2371067/52‑1 (MQ=255)
                                   gtTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAagaga                                                                  >  1:3844852/1‑40 (MQ=255)
                                    ttAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAagaga                                                                  >  1:3323775/1‑39 (MQ=255)
                                    ttAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATg                                  <  1:2195597/71‑1 (MQ=255)
                                    ttAGCCGATCGGCGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATg                                  <  1:1069319/71‑1 (MQ=255)
                                      aGCCGATCGGCGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTa                                >  1:1928609/1‑71 (MQ=255)
                                      aGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAgagattagagatta                                                        >  1:5036124/1‑47 (MQ=255)
                                          gATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACgg                             >  1:5093410/1‑70 (MQ=255)
                                           aTCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTc                                        <  1:2379490/58‑1 (MQ=255)
                                           aTCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTc                                        <  1:4269330/58‑1 (MQ=255)
                                              ggCGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGaa                        <  1:5064353/71‑1 (MQ=255)
                                              ggCGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGaa                        <  1:3790071/71‑1 (MQ=255)
                                                cGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGaa                        >  1:4597164/1‑69 (MQ=255)
                                                cGAAAGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGaa                        >  1:2246566/1‑69 (MQ=255)
                                                cGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTa                                    >  1:3845878/1‑57 (MQ=255)
                                                cGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTa                                    >  1:3057752/1‑57 (MQ=255)
                                                cGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTa                                    >  1:1374947/1‑57 (MQ=255)
                                                cGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACAGCAGaa                        >  1:194093/1‑69 (MQ=255)
                                                 gAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAg                     <  1:2794734/71‑1 (MQ=255)
                                                  aaaTGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGaa                        <  1:2307882/67‑1 (MQ=255)
                                                  aaaGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTaa                                                <  1:4895447/43‑1 (MQ=255)
                                                  aaaGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGaa                        <  1:1776698/67‑1 (MQ=255)
                                                  aaaGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAg                     >  1:2858342/1‑70 (MQ=255)
                                                  aaaGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAg                     >  1:1857536/1‑70 (MQ=255)
                                                  aaaGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGt                    <  1:301419/71‑1 (MQ=255)
                                                    aGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTa                                >  1:3571127/1‑57 (MQ=255)
                                                    aGGGCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTa                   >  1:1300043/1‑70 (MQ=255)
                                                    aGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTa                   >  1:564187/1‑70 (MQ=255)
                                                      ggCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTAAAg                >  1:5065179/1‑71 (MQ=255)
                                                       gCTGGGTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTa                                    >  1:933951/1‑50 (MQ=255)
                                                            gTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTgat                                         >  1:1275532/1‑38 (MQ=38)
                                                            gTTATGAAGAAGAGATTAGAGATTACGGGTTAAATCTGtt                                         >  1:3311406/1‑40 (MQ=255)
                                                            gTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATg                                  <  1:2509605/47‑1 (MQ=255)
                                                                 gAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTa                                >  1:3035721/1‑44 (MQ=255)
                                                                  aaaaaGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTa                   >  1:3996342/1‑56 (MQ=255)
                                                                    aaaGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTAAAGCTATCCCATTCTGa  <  1:4884223/71‑1 (MQ=255)
                                                                    |                                                                      
CATTTTGTCGAGTGTCTAAATTAAATGACGCTGGTGTTAGCCGATCGGCGAAAGGGCTGGGTTATGAAAAAGAGATTAGAGATTACGGGTTAAATCTGTTCGGTATGTACGGCAGAAAAGTAAAGCTATCCCATTCTGA  >  W3110S.gb/527591‑527729

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