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 F3 I0 R1 560 56.4 4650532 94.9% 4413354 59.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,998,196 A→G 10.6% Y454H (TAT→CAT)  yhiP ← predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,998,1960AG10.6% 223.6 / 16.5 85Y454H (TAT→CAT) yhiPpredicted transporter
Reads supporting (aligned to +/- strand):  ref base A (39/37);  new base G (5/4);  total (44/41)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.89e-01

GCACCATCAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTGCCACATAGCCGCC  >  W3110S.gb/3998127‑3998265
                                                                     |                                                                     
gCACCATCAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAg                                                                      <  1:3096144/71‑1 (MQ=255)
   ccATCAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACg                                                                   <  1:3004715/71‑1 (MQ=255)
     aTCAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACggg                                                                 >  1:350633/1‑71 (MQ=255)
     aTCAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACggg                                                                 >  1:3613548/1‑71 (MQ=255)
     aTCAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACggg                                                                 >  1:1634122/1‑71 (MQ=255)
      tCAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGa                                                                     <  1:4012742/66‑1 (MQ=255)
      tCAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACggg                                                                 >  1:871833/1‑70 (MQ=255)
      tCAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACggg                                                                 >  1:1830606/1‑70 (MQ=255)
      tCAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACggg                                                                 >  1:1943330/1‑70 (MQ=255)
      tCAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACggg                                                                 >  1:2432988/1‑70 (MQ=255)
       cAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGc                                                                >  1:821401/1‑70 (MQ=255)
        aaCAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGtata                                                                       >  1:1436961/1‑62 (MQ=255)
        aaCAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCaa                                                              >  1:284585/1‑71 (MQ=255)
        aaCAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCaa                                                              >  1:4038842/1‑71 (MQ=255)
         aCAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAAc                                                             <  1:1162069/71‑1 (MQ=255)
          cAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACg                                                            >  1:1878075/1‑71 (MQ=255)
          cAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACg                                                            >  1:3054640/1‑71 (MQ=255)
          cAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACg                                                            >  1:179262/1‑71 (MQ=255)
            gCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGtc                                                          <  1:4000115/71‑1 (MQ=255)
             cATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGtct                                                         >  1:606205/1‑71 (MQ=255)
              aTCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGtctc                                                        <  1:3168683/71‑1 (MQ=255)
               tCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGtata                                                                       <  1:539926/55‑1 (MQ=255)
               tCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGtata                                                                       <  1:3442999/55‑1 (MQ=255)
               tCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCa                                                       <  1:4095775/71‑1 (MQ=255)
                 actactGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGa                                                                     >  1:575970/1‑55 (MQ=255)
                 actactGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACgg                                                                  >  1:2866173/1‑58 (MQ=255)
                 actactGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCaa                                                              >  1:4575211/1‑62 (MQ=255)
                 actactGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGt                                                           >  1:3818029/1‑65 (MQ=255)
                 actactGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGt                                                           >  1:4076473/1‑65 (MQ=255)
                 actactGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAg                                                     >  1:3431713/1‑71 (MQ=255)
                  ctactGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGc                                                    >  1:3965039/1‑71 (MQ=255)
                     ctGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACTGGCAACGTCTCAAGCgg                                                  <  1:2957101/70‑1 (MQ=255)
                     ctGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCgg                                                  <  1:3360937/70‑1 (MQ=255)
                     ctGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCgg                                                  <  1:3275541/70‑1 (MQ=255)
                     ctGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGa                                                 >  1:1546084/1‑71 (MQ=255)
                          aCGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATGGACGGGCAACGTCTCAAGCGGATCgg                                             >  1:2170625/1‑70 (MQ=255)
                          aCGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCgg                                             >  1:3766600/1‑70 (MQ=255)
                           cGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGtata                                                                       <  1:4211045/43‑1 (MQ=255)
                           cGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGtata                                                                       <  1:1004762/43‑1 (MQ=255)
                           cGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGtata                                                                       <  1:446368/43‑1 (MQ=255)
                           cGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTa                                           <  1:2561492/71‑1 (MQ=255)
                           cGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTa                                           <  1:1720031/71‑1 (MQ=255)
                            gCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATGGACGGGCAACGTCTCAAGCGGATCGGTaa                                          >  1:497244/1‑71 (MQ=255)
                            gCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATGGA‑GGGCAACGTCTCAAGCGGATCGGTAAt                                         >  1:4526890/1‑71 (MQ=255)
                             cccAGCGTGACCAGCCCAATCTTACCAAACACGTTGGTATAGACGGGCAACGt                                                           >  1:4347476/1‑53 (MQ=255)
                             cccAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGt                                                           >  1:4047297/1‑53 (MQ=255)
                             cccAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTaa                                          >  1:1939821/1‑70 (MQ=255)
                             cccAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAAt                                         <  1:1126104/71‑1 (MQ=255)
                              ccAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGTATCGGTAAtg                                        <  1:1792270/71‑1 (MQ=255)
                                 gCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGa                                                                     <  1:1698400/39‑1 (MQ=255)
                                 gCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAAtgttg                                     <  1:2829511/71‑1 (MQ=255)
                                   gTGACCAGACCAATCTTACCAAACACGTTGGTATGGACGGGCAACGTCTCa                                                       <  1:4171384/51‑1 (MQ=255)
                                    tGACCAGACCAATCTTACCAAACACGTTGGTATGGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTcc                                  <  1:3881587/71‑1 (MQ=255)
                                    tGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGt                                            <  1:1007204/61‑1 (MQ=255)
                                    tGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTcc                                  <  1:1797858/71‑1 (MQ=255)
                                    tGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTc                                   <  1:1438087/70‑1 (MQ=255)
                                     gaccagaccaATCTTACCAAACACGTTGGTATAGACGGGCaa                                                              >  1:3202849/1‑42 (MQ=255)
                                     gaccagaccaATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCg                                                   >  1:3208353/1‑53 (MQ=255)
                                      accagaccaATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTaa                                          >  1:2014097/1‑61 (MQ=255)
                                          gaccaATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTcc                                  >  1:1030750/1‑65 (MQ=255)
                                             caATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCa                              >  1:3865223/1‑66 (MQ=255)
                                                tCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAAtgttg                                     <  1:966825/56‑1 (MQ=255)
                                                tCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAAtgttg                                     <  1:2217767/56‑1 (MQ=255)
                                                 cTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCgg                                                  <  1:160640/42‑1 (MQ=255)
                                                 cTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAAtgttgt                                    >  1:3668911/1‑56 (MQ=255)
                                                  ttACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTa                                           <  1:3611903/48‑1 (MQ=255)
                                                  ttACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTa                                           <  1:2975962/48‑1 (MQ=255)
                                                    aCCAAACACGTTGGTATGGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATg                  >  1:997704/1‑71 (MQ=255)
                                                    aCCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTc                                   >  1:2502561/1‑54 (MQ=255)
                                                    aCCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCa                              >  1:1941035/1‑59 (MQ=255)
                                                    aCCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAAt                   <  1:1643637/70‑1 (MQ=255)
                                                     ccAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGt                 >  1:980284/1‑71 (MQ=255)
                                                      cAAACACGTTGGTATGGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTc                                   >  1:2528204/1‑52 (MQ=255)
                                                      cAAACACGTTGGTATGGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGtt                <  1:2218627/71‑1 (MQ=255)
                                                      cAAACACGTTGGTATGGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGtt                <  1:939755/71‑1 (MQ=255)
                                                      cAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAAt                                         <  1:211496/46‑1 (MQ=255)
                                                      cAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGtt                <  1:979849/71‑1 (MQ=255)
                                                        aaCACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTGc              <  1:2246357/71‑1 (MQ=255)
                                                          cacGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTGCca            <  1:3245283/71‑1 (MQ=255)
                                                          cacGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTGCca            <  1:4030527/71‑1 (MQ=255)
                                                          cacGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTGCca            <  1:4602661/71‑1 (MQ=255)
                                                          cacGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTGCca            <  1:4577245/71‑1 (MQ=255)
                                                          cacGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTGCca            <  1:1905959/71‑1 (MQ=255)
                                                          cacGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGATGTCCGGCACCGCGGTAAATGTTGCca            >  1:860389/1‑71 (MQ=255)
                                                          cacGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATCTTGTCCGGCACCGCGGTAAATGTTGCca            >  1:3979405/1‑71 (MQ=255)
                                                           acGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCgg                                <  1:1214109/50‑1 (MQ=255)
                                                           acGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTg               <  1:1058226/67‑1 (MQ=255)
                                                             gTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTGCCACAt         <  1:1348139/71‑1 (MQ=255)
                                                              ttGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTGCcaca          >  1:1927743/1‑69 (MQ=255)
                                                               tGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCgg                                <  1:1908281/46‑1 (MQ=255)
                                                                ggTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTGCCACATAgc      >  1:3639527/1‑71 (MQ=255)
                                                                    taGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTaaa                    >  1:268987/1‑53 (MQ=255)
                                                                     aGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTGCCACATAgccgcc  >  1:1864519/1‑70 (MQ=255)
                                                                     |                                                                     
GCACCATCAACAGCATCACTACTGCAACGCCCAGCGTGACCAGACCAATCTTACCAAACACGTTGGTATAGACGGGCAACGTCTCAAGCGGATCGGTAATGTTGTCCGGCACCGCGGTAAATGTTGCCACATAGCCGCC  >  W3110S.gb/3998127‑3998265

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A