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 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,727,747 T→C 11.7% V168V (GTT→GTC)  pstA → phosphate transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,727,7470TC11.7% 206.6 / 18.3 77V168V (GTT→GTC) pstAphosphate transporter subunit
Reads supporting (aligned to +/- strand):  ref base T (45/23);  new base C (5/4);  total (50/27)
Fisher's exact test for biased strand distribution p-value = 7.12e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

GGCGCAGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATGCGCTGGG  >  W3110S.gb/3727678‑3727815
                                                                     |                                                                    
ggCGCAGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTa                                                                     >  1:1054448/1‑71 (MQ=255)
  cgcAGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCGTGGCGTTGTTGCAGGTGCCGATTGTTATc                                                                   >  1:3090734/1‑71 (MQ=255)
  cgcAGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTCATc                                                                   <  1:1981638/71‑1 (MQ=255)
  cgcAGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTCATc                                                                   <  1:1383733/71‑1 (MQ=255)
     aGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCg                                                                 >  1:2133580/1‑70 (MQ=255)
     aGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCg                                                                 >  1:3128970/1‑70 (MQ=255)
                 tctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGtt                                                                      <  1:4244723/53‑1 (MQ=255)
                 tctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCaccacc                                                          >  1:148190/1‑65 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGaa                                                     <  1:3269966/69‑1 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAAc                                                    >  1:2219241/1‑70 (MQ=255)
                  ctcCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACa                                                   >  1:3193912/1‑71 (MQ=255)
                    ccGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATg                                                 >  1:2785707/1‑71 (MQ=255)
                     cGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCga                                                        <  1:2096203/63‑1 (MQ=255)
                          gggcgggcGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGaaa                                           >  1:3235696/1‑71 (MQ=255)
                           ggcgggcgTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTAt                                                                    >  1:2394227/1‑45 (MQ=255)
                                gcgTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAAc                                                    >  1:1616430/1‑56 (MQ=255)
                                gcgTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTg                                     >  1:135200/1‑71 (MQ=255)
                                  gTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGcc                                   >  1:4145061/1‑71 (MQ=255)
                                  gTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGcc                                   >  1:2556759/1‑71 (MQ=255)
                                    gATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGa                                             <  1:4376946/59‑1 (MQ=255)
                                     aTTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCgaga                                                      >  1:1080295/1‑49 (MQ=255)
                                     aTTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTa                                <  1:4114750/71‑1 (MQ=255)
                                     aTTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGACGTa                                >  1:1566807/1‑71 (MQ=255)
                                      ttGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTa                                >  1:1899624/1‑70 (MQ=255)
                                      ttGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTa                                >  1:702200/1‑70 (MQ=255)
                                      ttGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTAc                               <  1:3496407/71‑1 (MQ=255)
                                        gCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACa                              <  1:2997848/70‑1 (MQ=255)
                                        gCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAg                             >  1:1674620/1‑71 (MQ=255)
                                         cccTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTg                                        <  1:3284386/59‑1 (MQ=255)
                                         cccTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGc                            >  1:4287249/1‑71 (MQ=255)
                                          ccTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGa                                             <  1:4178692/53‑1 (MQ=255)
                                           cTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGaaa                                           >  1:4508557/1‑54 (MQ=255)
                                           cTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCt                          >  1:28075/1‑71 (MQ=255)
                                           cTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCt                          >  1:1349512/1‑71 (MQ=255)
                                            tGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCt                          >  1:4432633/1‑70 (MQ=255)
                                            tGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACAACCGAGAACATGCTGAAACTGGTGCCGTACAGcc                           <  1:3622861/69‑1 (MQ=255)
                                             ggCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGaaa                                           >  1:2195056/1‑52 (MQ=255)
                                             ggCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGc                        >  1:3727609/1‑71 (MQ=255)
                                              gCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGc                        <  1:2767411/70‑1 (MQ=255)
                                              gCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCg                       >  1:3961746/1‑71 (MQ=255)
                                                gttgttGCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGt                      >  1:472925/1‑70 (MQ=255)
                                                gttgttGCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGt                      >  1:1228407/1‑70 (MQ=255)
                                                gttgttGCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGt                      >  1:1161325/1‑70 (MQ=255)
                                                 ttgttgCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGa                    <  1:433906/71‑1 (MQ=255)
                                                  tgttgCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGt                      >  1:833723/1‑68 (MQ=255)
                                                  tgttgCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTg                     >  1:730935/1‑69 (MQ=255)
                                                  tgttgCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTg                     >  1:1434599/1‑69 (MQ=255)
                                                   gttgCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGaa                   <  1:1505901/70‑1 (MQ=255)
                                                      gCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGTTGCCTTACAGCCTGCGTGAAGCg                <  1:227247/70‑1 (MQ=255)
                                                      gCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTg                         >  1:4367254/1‑61 (MQ=255)
                                                      gCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCgg               >  1:948603/1‑71 (MQ=255)
                                                      gCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCgg               >  1:2089604/1‑71 (MQ=255)
                                                      gCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCg                <  1:270098/70‑1 (MQ=255)
                                                      gCAGGTGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCgg               >  1:3062638/1‑71 (MQ=255)
                                                         ggTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCtt            <  1:2745367/71‑1 (MQ=255)
                                                          gTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGc                            <  1:2475139/54‑1 (MQ=255)
                                                          gTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTa           <  1:2673356/71‑1 (MQ=255)
                                                          gTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTa           <  1:292399/71‑1 (MQ=255)
                                                           tGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTAt          <  1:1838416/71‑1 (MQ=255)
                                                           tGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTAt          <  1:4220221/71‑1 (MQ=255)
                                                           tGCCGATTGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCTTACAGCCTGCGTGAAGCGGCTTAt          <  1:3082069/71‑1 (MQ=255)
                                                            gCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCgg               >  1:427303/1‑65 (MQ=255)
                                                              cGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGt                                      >  1:285828/1‑40 (MQ=255)
                                                              cGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGt                                      >  1:2349614/1‑40 (MQ=255)
                                                               gATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATgcgc      <  1:1440948/71‑1 (MQ=255)
                                                               gATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATgcgc      <  1:3079525/71‑1 (MQ=255)
                                                               gATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATgcgc      >  1:1788505/1‑71 (MQ=255)
                                                                aTTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAg                  >  1:4379825/1‑58 (MQ=255)
                                                                aTTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCgg               >  1:2635596/1‑61 (MQ=255)
                                                                aTTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATGCGCt     <  1:516869/71‑1 (MQ=255)
                                                                 ttGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAg                  >  1:2056760/1‑57 (MQ=255)
                                                                 ttGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAg                  >  1:160817/1‑57 (MQ=255)
                                                                 ttGTCATCCGCACCACCGAGAACATGCTGAAACTGGTg                                     >  1:1607290/1‑38 (MQ=255)
                                                                 ttGTCATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATGCGCTg    <  1:3293128/71‑1 (MQ=255)
                                                                  tGTTATCCGCACCACCGAGAACATGCTGAAACTgg                                       >  1:1269258/1‑35 (MQ=255)
                                                                  tGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATGCGCTgg   >  1:774447/1‑71 (MQ=255)
                                                                   gTTATCCGCACCACCGAGAACATGCTGAAACTGGTGcc                                   >  1:3673481/1‑38 (MQ=255)
                                                                   gTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATGCGCTggg  >  1:3062540/1‑71 (MQ=255)
                                                                     |                                                                    
GGCGCAGATGGAGCACTTCTCCGGCTGGGCGGGCGTGATTGCCCTGGCGTTGTTGCAGGTGCCGATTGTTATCCGCACCACCGAGAACATGCTGAAACTGGTGCCGTACAGCCTGCGTGAAGCGGCTTATGCGCTGGG  >  W3110S.gb/3727678‑3727815

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