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
A1 F8 I0 R1 311 50.1 4085234 95.9% 3917739 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 330,966 T→G 13.7% intergenic (+246/‑629) betT → / → yahA choline transporter of high affinity/predicted DNA‑binding transcriptional regulator

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb330,9660TG13.7% 228.2 / 47.9 118intergenic (+246/‑629)betT/yahAcholine transporter of high affinity/predicted DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base T (47/54);  new base G (9/7);  total (57/61)
Fisher's exact test for biased strand distribution p-value = 5.92e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.76e-01

Only 100 of 127 total aligned reads displayed.

TTCAATAAGTTTAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATCTGTGTGTGATA  >  W3110S.gb/330896‑331035
                                                                      |                                                                     
ttCAATAAGTTTAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAAt                                                                       >  1:85694/1‑71 (MQ=255)
ttCAATAAGTTTAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAAt                                                                       >  1:433033/1‑71 (MQ=255)
 tCAATAAGTTTAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAAtg                                                                      >  1:971670/1‑71 (MQ=255)
 tCAATAAGTTTAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAAtg                                                                      >  1:2812325/1‑71 (MQ=255)
  cAATAAGTTTAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAAtgt                                                                     >  1:2349152/1‑71 (MQ=255)
  cAATAAGTTTAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAAtgt                                                                     >  1:3104822/1‑71 (MQ=255)
    aTAAGTTTAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATgtgt                                                                   <  1:242761/71‑1 (MQ=255)
    aTAAGTTTAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATgtgt                                                                   <  1:1663673/71‑1 (MQ=255)
           tAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTa                                                             <  1:1395591/70‑1 (MQ=255)
           tAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAAGGTGTATCGTa                                                             >  1:2244711/1‑70 (MQ=255)
           tAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAAGGTGTATCGTa                                                             >  1:333761/1‑70 (MQ=255)
              tCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATc                                                         <  1:41429/71‑1 (MQ=255)
              tCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATc                                                         <  1:3855697/71‑1 (MQ=255)
              tCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATc                                                         <  1:557967/71‑1 (MQ=255)
                ttATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCaa                                                       >  1:587433/1‑71 (MQ=255)
                ttATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCaa                                                       >  1:868787/1‑71 (MQ=255)
                ttATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAAGGTGTATCGTAAATCaa                                                       >  1:1194460/1‑71 (MQ=255)
                     tAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGa                                                   <  1:1372542/70‑1 (MQ=255)
                     tAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGa                                                   <  1:2612025/70‑1 (MQ=255)
                     tAATGTAAATATTGATGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGa                                                   <  1:2160953/70‑1 (MQ=255)
                        tGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAAtt                                               <  1:3624943/71‑1 (MQ=255)
                          tAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTaaa                                                           >  1:145102/1‑57 (MQ=255)
                          tAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTaa                                             >  1:2351321/1‑71 (MQ=255)
                          tAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTa                                              <  1:2863459/70‑1 (MQ=255)
                          tAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTa                                              <  1:709268/70‑1 (MQ=255)
                          tAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTa                                              <  1:2104034/70‑1 (MQ=255)
                          tAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTa                                              <  1:2023011/70‑1 (MQ=255)
                          tAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAAGGTGTATCGTAAATCAACTGAAATTaa                                             <  1:423716/71‑1 (MQ=255)
                          tAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAAGGTGTATCGTAAATCAACTGAAATTaa                                             >  1:3912421/1‑71 (MQ=255)
                            aaTATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACg                                           >  1:3801557/1‑71 (MQ=255)
                            aaTATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACg                                           >  1:1006360/1‑71 (MQ=255)
                            aaTATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACg                                           >  1:3620562/1‑71 (MQ=255)
                            aaTATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACg                                           >  1:3909480/1‑71 (MQ=255)
                               atTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCaa                                        >  1:3075767/1‑71 (MQ=255)
                                ttGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTaa                                                            >  1:3919703/1‑50 (MQ=255)
                                ttGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAAc                                                      >  1:1132823/1‑56 (MQ=255)
                                ttGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGa                                                   <  1:1735329/59‑1 (MQ=255)
                                  gCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCa                                     >  1:861268/1‑71 (MQ=255)
                                  gCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCa                                     >  1:2599266/1‑71 (MQ=255)
                                  gCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCa                                     >  1:4038733/1‑71 (MQ=255)
                                    tGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCa                                         <  1:2816067/65‑1 (MQ=255)
                                      aTCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTg                                                    <  1:1642698/52‑1 (MQ=255)
                                      aTCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCa                                         <  1:362205/63‑1 (MQ=255)
                                      aTCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCa                                         <  1:561340/63‑1 (MQ=255)
                                      aTCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCAtt                                   <  1:3452930/69‑1 (MQ=255)
                                       tCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCa                                         <  1:2759003/62‑1 (MQ=255)
                                       tCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTg                                 <  1:2036259/70‑1 (MQ=255)
                                        cATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGt                                >  1:3802838/1‑70 (MQ=255)
                                        cATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGt                                >  1:956225/1‑70 (MQ=255)
                                        cATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGt                                >  1:1398715/1‑70 (MQ=255)
                                         aTTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTa                              >  1:1732220/1‑71 (MQ=255)
                                         aTTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTa                              >  1:64650/1‑71 (MQ=255)
                                         aTTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTa                              >  1:3941343/1‑71 (MQ=255)
                                            tGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTAtt                            >  1:1249206/1‑70 (MQ=255)
                                              aaaTGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTa                          <  1:1770101/70‑1 (MQ=255)
                                                   aCGCATTATTCATGAGAAATGTGTATCGTAAATCaa                                                       >  1:2214657/1‑36 (MQ=255)
                                                   aCGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTAtt                            >  1:789860/1‑63 (MQ=255)
                                                   aCGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGtt                     >  1:1789894/1‑70 (MQ=255)
                                                   aCGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGtt                     >  1:1445888/1‑70 (MQ=255)
                                                   aCGCATTATTCATGAGAAAGGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGtt                     >  1:2813042/1‑70 (MQ=255)
                                                    cGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTa                   <  1:2515125/71‑1 (MQ=255)
                                                    cGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTa                   <  1:2376186/71‑1 (MQ=255)
                                                        ttattCATGAGAAATGTGTATCGTAAATCAACTGAAAt                                                <  1:3081096/38‑1 (MQ=255)
                                                        ttattCATGAGAAATGTGTATCGTAAATCAACTGAAAt                                                <  1:1374861/38‑1 (MQ=255)
                                                        ttattCATGAGAAATGTGTATCGTAAATCAACTGAAAt                                                <  1:1980298/38‑1 (MQ=255)
                                                        ttattCATGAGAAATGTGTATCGTAAATCAACTGAAAt                                                <  1:2849579/38‑1 (MQ=255)
                                                        ttattCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGc                                          <  1:3503782/44‑1 (MQ=255)
                                                        ttattCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTa               >  1:1589764/1‑71 (MQ=255)
                                                         tattCATGAGAAATGTGTATCGTAAATCAACTGAAAtt                                               <  1:3875666/38‑1 (MQ=255)
                                                          attGATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAgg                       >  1:522085/1‑61 (MQ=255)
                                                          attCATGAGAAATGTGTATCGTAAATCAACTGAAATTAAc                                            >  1:3577638/1‑40 (MQ=255)
                                                          attCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAgg                       >  1:2185289/1‑61 (MQ=255)
                                                          attCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAgg                       >  1:578817/1‑61 (MQ=255)
                                                          attCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAgg                       >  1:488104/1‑61 (MQ=255)
                                                          attCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAg                        >  1:3316487/1‑60 (MQ=255)
                                                          attCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAg                        >  1:3016189/1‑60 (MQ=255)
                                                          attCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAg                        >  1:2754997/1‑60 (MQ=255)
                                                          attCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAg                        >  1:2510858/1‑60 (MQ=255)
                                                          attCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATc             >  1:2228051/1‑71 (MQ=255)
                                                          attCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATc             >  1:625020/1‑71 (MQ=255)
                                                          attCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATc             >  1:2765603/1‑71 (MQ=255)
                                                          attCATGAGAAAGGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATc             >  1:943356/1‑71 (MQ=255)
                                                           ttCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATCt            >  1:2474517/1‑71 (MQ=255)
                                                           ttCATGAGAAAGGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATCt            >  1:2583071/1‑71 (MQ=255)
                                                             cATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATCtgt          >  1:740393/1‑71 (MQ=255)
                                                             cATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATCtg           <  1:835315/70‑1 (MQ=255)
                                                              aTGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATCtgt          <  1:3633758/70‑1 (MQ=255)
                                                                gagaAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATCtgtgtg       >  1:4064592/1‑71 (MQ=255)
                                                                 agaAAGGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGt                      >  1:1540419/1‑55 (MQ=255)
                                                                 agaAAGGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGt                      >  1:1963599/1‑55 (MQ=255)
                                                                 agaAAGGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATCtgtgtgt      <  1:1049834/71‑1 (MQ=255)
                                                                  gaAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATCtgtgtgtg     <  1:3313972/71‑1 (MQ=255)
                                                                     aTGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGttt                     <  1:2460384/52‑1 (MQ=255)
                                                                     aTGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGtt                     <  1:1022881/52‑1 (MQ=255)
                                                                     aTGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGtt                     <  1:886186/52‑1 (MQ=255)
                                                                     aTGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGtt                     <  1:1988220/52‑1 (MQ=255)
                                                                     aTGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGtt                     <  1:2871289/52‑1 (MQ=255)
                                                                     aTGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATCTGTGTGTGata  <  1:2429249/71‑1 (MQ=255)
                                                                      tgtgTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGttt                    <  1:3281545/52‑1 (MQ=255)
                                                                      tgtgTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGttt                    <  1:618885/52‑1 (MQ=255)
                                                                      |                                                                     
TTCAATAAGTTTAGTCTTATTTAATGTAAATATTGCTGATCATTTGAAATGACGCATTATTCATGAGAAATGTGTATCGTAAATCAACTGAAATTAACGCAACCATTTGTTATTTAAGGTTTAATTATCTGTGTGTGATA  >  W3110S.gb/330896‑331035

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