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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 386,420 A→G 23.6% I544V (ATT→GTT)  cstA → carbon starvation protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE386,4200AG23.6% 169.3 / 50.1 93I544V (ATT→GTT) cstAcarbon starvation protein
Reads supporting (aligned to +/- strand):  ref base A (40/31);  new base G (18/4);  total (58/35)
Fisher's exact test for biased strand distribution p-value = 4.32e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.14e-01

GCAACAGCGCTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGC  >  minE/386351‑386483
                                                                     |                                                               
gCAACAGCGCTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCAt                                                                <  1:1353809/71‑1 (MQ=255)
     aGCGCTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAaca                                                           >  1:3332413/1‑71 (MQ=255)
     aGCGCTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAaca                                                           >  1:2785264/1‑71 (MQ=255)
     aGCGCTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAaca                                                           >  1:2280740/1‑71 (MQ=255)
     aGCGCTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAaca                                                           >  1:15669/1‑71 (MQ=255)
       cgcTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACAct                                                         >  1:4569652/1‑71 (MQ=255)
       cgcTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACAct                                                         <  1:3681459/71‑1 (MQ=255)
       cgcTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACAct                                                         <  1:4234938/71‑1 (MQ=255)
       cgcTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACAct                                                         <  1:5171616/71‑1 (MQ=255)
        gcTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAaca                                                           <  1:2365723/68‑1 (MQ=255)
         cTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACActct                                                       >  1:1258156/1‑71 (MQ=255)
         cTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACActct                                                       >  1:1434803/1‑71 (MQ=255)
          tgtgCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACAct                                                         >  1:4495123/1‑68 (MQ=255)
          tgtgCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACAct                                                         >  1:2042437/1‑68 (MQ=255)
            tgCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCtg                                                      <  1:4539334/69‑1 (MQ=255)
            tgCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGACCCGCTGGGCGGCATTAACACTCtg                                                      <  1:5365051/69‑1 (MQ=255)
                tACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCg                                                <  1:4755316/71‑1 (MQ=255)
                  cTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCtgtg                                                    >  1:2113715/1‑65 (MQ=255)
                    ggCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGt                                            >  1:5405944/1‑71 (MQ=255)
                     ctgTGGGGCTACCTGCTGTATCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGtt                                           >  1:4246239/3‑71 (MQ=255)
                      cGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGttt                                          <  1:1226240/71‑1 (MQ=255)
                        tGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTgg                                        <  1:461061/71‑1 (MQ=255)
                        tGGGGCTACCTGCTGTATCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTgg                                                   >  1:1617627/1‑60 (MQ=255)
                        tGGGGCTACCTGCTGTATCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTgg                                                   >  1:3887993/1‑60 (MQ=255)
                        tGGGGCTACCTGCTGTATCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGttcg                                         <  1:4717093/70‑3 (MQ=255)
                        tGGGGCTACCTGCTGTATCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCgg                                        >  1:631643/1‑71 (MQ=255)
                           ggCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTAt                                     >  1:3791246/1‑71 (MQ=255)
                           ggCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTAt                                     <  1:143491/71‑1 (MQ=255)
                               aCTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACActc                                                        <  1:2358133/48‑1 (MQ=255)
                                cTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTaa                                                             <  1:4343976/42‑1 (MQ=255)
                                cTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCtg                                                      >  1:2041384/1‑49 (MQ=255)
                                cTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCt                                              <  1:3705264/57‑1 (MQ=255)
                                 ttCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGt                                            <  1:4154420/58‑1 (MQ=255)
                                 ttCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCaa                               >  1:3665008/1‑71 (MQ=255)
                                  tcctccATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAAc                              >  1:568502/1‑71 (MQ=255)
                                   cctccATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGttt                                          >  1:1398909/1‑58 (MQ=255)
                                   cctccATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTa                                      >  1:405259/1‑62 (MQ=255)
                                     tgtaTCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTAt                                     >  1:469441/4‑61 (MQ=255)
                                      ccATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTa                                      >  1:5199583/1‑59 (MQ=255)
                                      ccATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTAt                                     >  1:4503111/1‑60 (MQ=255)
                                      ccATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTAt                                     >  1:2478397/1‑60 (MQ=255)
                                       taTCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGa                          <  1:4894737/69‑1 (MQ=255)
                                       cATCAGGGCGTGGTCGATCCGCTGGGCGGCATTaa                                                             >  1:5108796/1‑35 (MQ=255)
                                       cATCAGGGCGTGGTCGATCCGCTGGGCGGCATTaa                                                             >  1:4169356/1‑35 (MQ=255)
                                       cATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTAtt                                    <  1:675295/60‑1 (MQ=255)
                                        aTCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGAt                         >  1:3166269/1‑70 (MQ=255)
                                        aTCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATg                        >  1:5089241/1‑71 (MQ=255)
                                         tCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCt                                              >  1:5307376/1‑48 (MQ=21)
                                         tCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCt                                              >  1:4005202/1‑48 (MQ=21)
                                         tCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCt                                              >  1:2601680/1‑48 (MQ=21)
                                         tCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCgg                                        >  1:21154/1‑54 (MQ=25)
                                         tCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGc                       <  1:3424525/71‑1 (MQ=255)
                                         tCAGGGCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGc                       >  1:512031/1‑71 (MQ=255)
                                         tCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTgg                                        <  1:5247843/54‑1 (MQ=255)
                                         tCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTgg                                        <  1:4409241/54‑1 (MQ=255)
                                         tCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAAc                              <  1:2615699/64‑1 (MQ=255)
                                         tCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAg                           <  1:3803587/67‑1 (MQ=255)
                                         tCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGc                       >  1:3092143/1‑71 (MQ=255)
                                           aGGTCGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGCTg                     >  1:4025979/1‑71 (MQ=19)
                                           aGGGCGTGGTCGATCCGCTGGGCGGGATCAACACCCTGTGGCCGCTGTTCGGCATCGCCAACCAGATGCTg                     >  1:598713/1‑71 (MQ=255)
                                           aGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTa                                      >  1:4872730/1‑54 (MQ=255)
                                           aGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTAtt                                    >  1:2362930/1‑56 (MQ=255)
                                           aGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTg                     >  1:892867/1‑71 (MQ=255)
                                           aGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTg                     >  1:764011/1‑71 (MQ=255)
                                               cGTGGTTGATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGCTGGCAg                 >  1:5376531/1‑71 (MQ=25)
                                               cGTGGTCGATCCGCTGGGCGGCATTAACACTCtgt                                                     >  1:2761479/1‑35 (MQ=255)
                                               cGTGGTCGATCCGCTGGGCGGCATTAACACTCtgt                                                     >  1:2767976/1‑35 (MQ=255)
                                               cGTGGTCGATCCGCTGGGCGGCATTAACACTCtgt                                                     >  1:315017/1‑35 (MQ=255)
                                               cGTGGTCGATCCGCTGGGCGGCATTAACACTCtgt                                                     >  1:3416126/1‑35 (MQ=255)
                                                gTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAgg                <  1:705262/71‑1 (MQ=255)
                                                gTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAgg                >  1:5403478/1‑71 (MQ=255)
                                                   gTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGttt                                          >  1:793803/1‑42 (MQ=255)
                                                   gTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGttt                                          >  1:5442634/1‑42 (MQ=255)
                                                   gTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGttt                                          >  1:1523083/1‑42 (MQ=255)
                                                   gTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGt                                       >  1:4778075/1‑45 (MQ=255)
                                                    ttgATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAAc                              >  1:943000/3‑53 (MQ=16)
                                                    ttgATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGCTgg                    <  1:3797837/61‑1 (MQ=19)
                                                     cGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTg                                         >  1:4795395/1‑41 (MQ=255)
                                                      gATCCGCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGt                                       >  1:3596631/1‑42 (MQ=19)
                                                      gATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTAt                                     <  1:1805577/44‑1 (MQ=255)
                                                      gATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGgc          <  1:2984461/71‑1 (MQ=255)
                                                          cGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCt       <  1:5444251/70‑1 (MQ=255)
                                                          cGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCt       <  1:5492450/70‑1 (MQ=255)
                                                           gCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGa                          >  1:2204434/1‑50 (MQ=255)
                                                           gCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGa                          >  1:146458/1‑50 (MQ=255)
                                                           gCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGCTgg                    >  1:1378796/1‑56 (MQ=16)
                                                           gCTGGGCGGCGTTAAGAGCCTGTGGCCGCTGTTCGGTATCTCCAACCAGATGCTgg                    >  1:4957401/1‑56 (MQ=16)
                                                           gCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGAt             <  1:2398335/63‑1 (MQ=255)
                                                           gCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCt       <  1:146810/69‑1 (MQ=255)
                                                           gCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCt       <  1:2758244/69‑1 (MQ=255)
                                                            cTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGAt             <  1:490666/62‑1 (MQ=255)
                                                               ggcggcATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATg   <  1:4941133/69‑1 (MQ=255)
                                                               ggcggcATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGc  <  1:1693235/70‑1 (MQ=255)
                                                                     |                                                               
GCAACAGCGCTGTGCGTACTGGCGTGGGGCTACTTCCTCCATCAGGGCGTGGTCGATCCGCTGGGCGGCATTAACACTCTGTGGCCGCTGTTTGGTATTGCCAACCAGATGCTGGCAGGGATGGCGCTGATGC  >  minE/386351‑386483

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A