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 4,350,232 G→A 43.5% R3C (CGC→TGC)  yjdF ← conserved inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,350,2320GA43.5% 41.6 / 109.5 85R3C (CGC→TGC) yjdFconserved inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (19/29);  new base A (8/29);  total (27/58)
Fisher's exact test for biased strand distribution p-value = 1.01e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.34e-02

ATGCCGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCGCAA  >  W3110S.gb/4350162‑4350302
                                                                      |                                                                      
aTGCCGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCg                                                                        >  1:320593/1‑71 (MQ=255)
 tGCCGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCgg                                                                       <  1:4240453/71‑1 (MQ=255)
  gCCGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCggg                                                                      >  1:4099524/1‑71 (MQ=255)
   ccGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGt                                                                     >  1:4697660/1‑71 (MQ=255)
   ccGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGt                                                                     >  1:2690030/1‑71 (MQ=255)
      gTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCAt                                                                  <  1:2318081/71‑1 (MQ=255)
      gTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCAt                                                                  <  1:2256120/71‑1 (MQ=255)
      gTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCAt                                                                  <  1:1915308/71‑1 (MQ=255)
       tataAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATg                                                                 <  1:231903/71‑1 (MQ=255)
       tataAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATg                                                                 <  1:646683/71‑1 (MQ=255)
       tataAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATg                                                                 <  1:34315/71‑1 (MQ=255)
         taAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCg                                                                        <  1:2944855/62‑1 (MQ=255)
         taAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCg                                                                        <  1:3540494/62‑1 (MQ=255)
           aaTCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGt                                                               >  1:4805170/1‑69 (MQ=255)
           aaTCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTg                                                              <  1:637289/70‑1 (MQ=255)
            aTCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAg                                                            <  1:3101546/71‑1 (MQ=255)
             tCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGt                                                               >  1:4923722/1‑67 (MQ=255)
             tCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGt                                                               >  1:3806560/1‑67 (MQ=255)
             tCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGt                                                           <  1:4462543/71‑1 (MQ=255)
             tCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGt                                                           >  1:597532/1‑71 (MQ=255)
             tCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGt                                                           <  1:609119/71‑1 (MQ=255)
             tCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGt                                                           <  1:2381480/71‑1 (MQ=255)
                   ttAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCa                                                      >  1:156334/1‑70 (MQ=255)
                     aaCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAAt                                                   >  1:2534703/1‑71 (MQ=255)
                     aaCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGAGGGTCATGGTGAGTTCGCAAAt                                                   >  1:2260234/1‑71 (MQ=255)
                      aCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGAAAAt                                                   <  1:931806/70‑1 (MQ=255)
                      aCGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATc                                                  <  1:339912/71‑1 (MQ=255)
                       cGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCa                                                 <  1:4197320/71‑1 (MQ=255)
                         ttAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAg                                                            <  1:4301115/58‑1 (MQ=255)
                           aGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCa                                                      <  1:2386816/62‑1 (MQ=255)
                           aGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCa                                                      <  1:111561/62‑1 (MQ=255)
                           aGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAggg                                              >  1:3278299/1‑70 (MQ=255)
                            gCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGaa                                            <  1:833357/71‑1 (MQ=255)
                             cGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGaa                                            <  1:4299108/70‑1 (MQ=255)
                              gTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGaaaa                                          <  1:3282008/71‑1 (MQ=255)
                               tCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCa                                                                   >  1:4564477/1‑45 (MQ=255)
                               tCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATc                                                  <  1:1118249/62‑1 (MQ=255)
                               tCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCaa                                                     <  1:1733450/59‑1 (MQ=255)
                                 aGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAg                                                >  1:4635193/1‑62 (MQ=255)
                                 aGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAg                                                >  1:130358/1‑62 (MQ=255)
                                  gTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACt                                      <  1:178229/71‑1 (MQ=255)
                                  gTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACt                                      <  1:4950051/71‑1 (MQ=255)
                                  gTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACt                                      <  1:4955977/71‑1 (MQ=255)
                                   tGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAAt                                         <  1:4389406/67‑1 (MQ=255)
                                   tGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCa                                                 <  1:3569360/59‑1 (MQ=255)
                                     cgcTGGTGTTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGAc                                   >  1:4527110/1‑71 (MQ=255)
                                          gtgtTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTAt                                <  1:2847108/69‑1 (MQ=255)
                                           tgtTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGaa                                            <  1:4549330/56‑1 (MQ=255)
                                           tgtTAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTc                              <  1:1617294/70‑1 (MQ=255)
                                             ttAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGa                                    >  1:3955103/1‑62 (MQ=255)
                                             ttAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGAc                                   <  1:259594/63‑1 (MQ=255)
                                             ttAAGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCa                                                      <  1:329546/44‑1 (MQ=255)
                                               aaGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAg                         >  1:332505/1‑71 (MQ=255)
                                                aGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAg                                                            <  1:1560775/35‑1 (MQ=255)
                                                aGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAg                                                            <  1:2571456/35‑1 (MQ=255)
                                                aGAATTAACGGCTTGAGTGTGCAGGTCATGGTGAg                                                            <  1:4249312/35‑1 (MQ=255)
                                                 gAATTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGaa                                            <  1:1522489/50‑1 (MQ=255)
                                                  aaTTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGc                        >  1:2205949/1‑69 (MQ=255)
                                                   aTTAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAg                     >  1:1599845/1‑71 (MQ=255)
                                                    ttAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCa                                                      <  1:699060/37‑1 (MQ=255)
                                                    ttAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAggg                                              <  1:3317264/45‑1 (MQ=255)
                                                    ttAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGaa                                            <  1:3197730/47‑1 (MQ=255)
                                                    ttAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGc                    >  1:872789/1‑71 (MQ=255)
                                                    ttAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGc                    >  1:2185026/1‑71 (MQ=255)
                                                     tAACGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGaaaa                                          <  1:59795/48‑1 (MQ=255)
                                                      aaCGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGaaaa                                          >  1:417487/1‑47 (MQ=255)
                                                      aaCGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGaaaa                                          >  1:2183204/1‑47 (MQ=255)
                                                      aaCGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCa                          >  1:1279533/1‑63 (MQ=255)
                                                       aCGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCa                                                 <  1:4211821/39‑1 (MQ=255)
                                                       aCGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCa                                                 <  1:2498508/39‑1 (MQ=255)
                                                       aCGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCa                                                 <  1:4061897/39‑1 (MQ=255)
                                                       aCGGCTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCa                                                 <  1:1716344/39‑1 (MQ=255)
                                                        cGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATAATGACTATTCACCAGCAAGCGTGa                <  1:4038791/71‑1 (MQ=255)
                                                          gCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGaa               <  1:4595182/70‑1 (MQ=255)
                                                           cTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGaaa              <  1:3440208/70‑1 (MQ=255)
                                                           cTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAAt             <  1:2124494/71‑1 (MQ=255)
                                                           cTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAAt             <  1:2341206/71‑1 (MQ=255)
                                                           cTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAAt             >  1:58690/1‑71 (MQ=255)
                                                           cTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCaa                      <  1:622618/62‑1 (MQ=255)
                                                           cTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAAt             <  1:1241843/71‑1 (MQ=255)
                                                           cTTGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAAt             <  1:4069979/71‑1 (MQ=255)
                                                            ttGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAg                                                >  1:557239/1‑35 (MQ=255)
                                                            ttGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATAc                                       >  1:590551/1‑44 (MQ=255)
                                                            ttGAGTGTGCAGGTCATGGTGAGTTCGCAAATCAGGGaa                                            <  1:1803023/39‑1 (MQ=255)
                                                                   tgCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCg     <  1:1715636/71‑1 (MQ=255)
                                                                   tgCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGa                <  1:146494/60‑1 (MQ=255)
                                                                   tgCAGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGa                <  1:3332254/60‑1 (MQ=255)
                                                                     cGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCGc    <  1:2166020/70‑1 (MQ=255)
                                                                     cGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCGc    <  1:1498172/70‑1 (MQ=255)
                                                                     cGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCGc    >  1:4350280/1‑70 (MQ=255)
                                                                      gggTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCGCaa  <  1:3605986/71‑1 (MQ=255)
                                                                      |                                                                      
ATGCCGGTATAAATCAGGATTAACGTTAGCGTCAGTGCGCTGGTGTTAAGAATTAACGGCTTGAGTGTGCGGGTCATGGTGAGTTCGCAAATCAGGGAAAATACTGACTATTCACCAGCAAGCGTGAAATTACAATCGCAA  >  W3110S.gb/4350162‑4350302

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