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 1,933,315 G→A 26.9% F376F (TTC→TTT)  lysS ← lysine tRNA synthetase, constitutive

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,933,3150GA26.9% 279.9 / 110.2 171F376F (TTC→TTT) lysSlysine tRNA synthetase, constitutive
Reads supporting (aligned to +/- strand):  ref base G (64/61);  new base A (20/26);  total (84/87)
Fisher's exact test for biased strand distribution p-value = 3.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.90e-02

Only 100 of 176 total aligned reads displayed.

GCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAAT  >  minE/1933245‑1933383
                                                                      |                                                                    
gCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCg                                                                      <  1:4607680/71‑1 (MQ=255)
       aaCTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAtct                                                               >  1:4452494/1‑71 (MQ=255)
         cTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAg                                                                   <  1:125500/65‑1 (MQ=255)
         cTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAg                                                                   <  1:157479/65‑1 (MQ=255)
          ttCTGCCGGATATTCCGTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGAtctctg                                                            >  1:1675878/1‑69 (MQ=255)
          ttCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCgg                                                            >  1:659157/1‑71 (MQ=255)
           tCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAt                                                                 >  1:2316289/1‑65 (MQ=255)
           tCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAt                                                                 >  1:4072003/1‑65 (MQ=255)
           tCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAt                                                                 >  1:3369534/1‑65 (MQ=255)
            cTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGt                                                           <  1:5263079/70‑1 (MQ=255)
            cTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGt                                                           >  1:1264060/1‑70 (MQ=255)
               ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                                                        <  1:2198002/70‑1 (MQ=255)
               ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                                                        <  1:3331715/70‑1 (MQ=255)
               ccGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                                                        <  1:5251145/70‑1 (MQ=255)
                cGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                      <  1:688790/71‑1 (MQ=255)
                 ggATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGAt                                                     <  1:4125749/71‑1 (MQ=255)
                      ttCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGAt                                                     <  1:3361860/66‑1 (MQ=255)
                       tCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGcc                                               >  1:3587386/1‑71 (MQ=255)
                        ccgTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTcc                                               >  1:228746/3‑70 (MQ=255)
                        ccgTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTcc                                               >  1:880591/3‑70 (MQ=255)
                        cAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGcc                                               >  1:1606530/1‑70 (MQ=255)
                         cgTAATAAAGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTccc                                              <  1:5349380/69‑1 (MQ=255)
                            aaTGAAGCTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAc                                          >  1:3738040/1‑71 (MQ=255)
                             aTGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcc                                         >  1:5092796/1‑71 (MQ=255)
                             aTGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcc                                         >  1:3130815/1‑71 (MQ=255)
                             aTGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcc                                         >  1:2666226/1‑71 (MQ=255)
                              tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAtc                                                                <  1:4082040/47‑1 (MQ=255)
                              tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGAtc                                                                <  1:3058260/47‑1 (MQ=255)
                              tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                      <  1:3930688/57‑1 (MQ=255)
                              tGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                      <  1:171847/57‑1 (MQ=255)
                                aaGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGAtctct                                                             >  1:1996093/1‑47 (MQ=37)
                                aaGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGAtctct                                                             >  1:3028351/1‑47 (MQ=37)
                                aaGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATa                                                    >  1:450541/1‑57 (MQ=255)
                                aaGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCa                                             >  1:25551/1‑64 (MQ=255)
                                aaGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAccc                                        >  1:1942019/1‑69 (MQ=255)
                                 aGGTTGGCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAg                                     <  1:375750/71‑1 (MQ=255)
                                    tCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                      >  1:3669043/1‑51 (MQ=255)
                                      ggCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAAc                                                        >  1:488872/1‑47 (MQ=255)
                                      ggCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAc                                          <  1:58183/61‑1 (MQ=255)
                                      ggCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAc                                          <  1:2444210/61‑1 (MQ=255)
                                      ggCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAc                                          <  1:545496/61‑1 (MQ=255)
                                      ggCTGAATCAGATGTGCTTCTGCCACTTCATCaaa                                                                    <  1:2522397/35‑1 (MQ=37)
                                      ggCTGAATCAGATGTGCTTCTGCCACTTCATCaaa                                                                    <  1:2374339/35‑1 (MQ=37)
                                      ggCTGAATCAGATGTGCTTCTGCCACTTCATCAAAg                                                                   <  1:5643474/36‑1 (MQ=37)
                                      ggCTGAATCAGATGTGCTTCTGCCACTTCATCAAAg                                                                   <  1:4648491/36‑1 (MQ=37)
                                      ggCTGAATCAGATGTGCTTCTGCCACTTCATCAAAg                                                                   <  1:1167873/36‑1 (MQ=37)
                                      ggCTGAATCAGATGTGCTTCTGCCACTTCATCAAAg                                                                   <  1:2047972/36‑1 (MQ=37)
                                      ggCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCa                                      >  1:1904783/1‑65 (MQ=255)
                                      ggCTGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCa                                      >  1:3610316/1‑65 (MQ=255)
                                       gCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                      <  1:3830996/48‑1 (MQ=255)
                                         tGAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAAt                                                     <  1:3573310/47‑1 (MQ=25)
                                          gAATCAGATGTGCTTCTGCCACTTCTTCGAATATCTCGGTAAAGa                                                      <  1:3153150/45‑1 (MQ=38)
                                          gAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGtga                                                         >  1:139788/1‑40 (MQ=25)
                                          gAATCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGtg                                                          >  1:2323336/1‑40 (MQ=25)
                                           aaTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcccc                                       >  1:1300250/1‑59 (MQ=255)
                                           aaTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTtctc                             <  1:3421519/69‑1 (MQ=255)
                                           aaTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCa                            <  1:3710205/70‑1 (MQ=255)
                                           aaTCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTtctcta                           >  1:1322916/1‑69 (MQ=255)
                                           aaTCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTtctc                             <  1:2721236/69‑1 (MQ=255)
                                           aaTCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTtctc                             <  1:1493536/69‑1 (MQ=255)
                                           aaTCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTtctc                             <  1:1853951/69‑1 (MQ=255)
                                            aTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcc                                         <  1:3894561/56‑1 (MQ=255)
                                            aTCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTtctc                             <  1:4173209/68‑1 (MQ=255)
                                            aTCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGAcaa                                                      >  1:5674402/1‑41 (MQ=21)
                                             tCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                      <  1:2143698/42‑1 (MQ=255)
                                             tCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                      <  1:215251/42‑1 (MQ=255)
                                             tCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGAcccc                                       >  1:4681172/1‑57 (MQ=255)
                                             tCAGATGTGCTTCTGCCACTTCATCAGAGATCTCTGTGAcaa                                                      <  1:5548482/42‑3 (MQ=16)
                                             tCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGAcaa                                                      <  1:4724694/42‑3 (MQ=21)
                                             tCAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTTCTCTAcc                         >  1:4148008/1‑70 (MQ=255)
                                              cAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGa                                                      <  1:2003497/41‑1 (MQ=255)
                                              cAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCaa                           >  1:1590314/1‑68 (MQ=255)
                                              cAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTtctc                             >  1:135385/1‑66 (MQ=255)
                                              cAGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTtctc                             >  1:50082/1‑66 (MQ=255)
                                               aGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGt                        <  1:2902844/70‑1 (MQ=255)
                                               aGATGTGCTTCTGCCACTTCATCAAAGATCTCTGTGACAATACGTCCCAACCCCCAGCTTTTCTCTAccgt                       <  1:3852109/71‑4 (MQ=255)
                                                gATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTgg                      <  1:4687913/71‑1 (MQ=255)
                                                  tgtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGAt                    <  1:5369291/71‑1 (MQ=255)
                                                  tgtgCTTCTGCCACTTCATCAAAGATCTCTGTAACAATACGTCCCa                                             <  1:4562239/46‑1 (MQ=25)
                                                   gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCa                                             >  1:1040531/1‑45 (MQ=255)
                                                   gtgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCtcttc                               >  1:4011272/1‑59 (MQ=255)
                                                    tgCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATg                   >  1:1089477/1‑70 (MQ=255)
                                                     gCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCa                            <  1:3461882/60‑1 (MQ=255)
                                                      cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCtcttc                               >  1:4239722/1‑56 (MQ=255)
                                                      cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGcc                 >  1:3481753/1‑70 (MQ=255)
                                                      cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGcc                 >  1:1536290/1‑70 (MQ=255)
                                                      cTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGcc                 >  1:1034932/1‑70 (MQ=255)
                                                        tCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCa                                             >  1:3955280/1‑40 (MQ=255)
                                                        tCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCa                                             >  1:2966395/1‑40 (MQ=255)
                                                         cTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGa               <  1:2313055/69‑1 (MQ=255)
                                                           gCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTtctc                             >  1:3801942/1‑53 (MQ=255)
                                                               cttcttCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGAtt         >  1:548779/1‑69 (MQ=255)
                                                               cttcttCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGAtt         >  1:5553026/1‑69 (MQ=255)
                                                                 tcttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAg      >  1:2793419/1‑70 (MQ=255)
                                                                 tcttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAg      >  1:296842/1‑70 (MQ=255)
                                                                  cttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGc     <  1:697422/70‑1 (MQ=255)
                                                                   ttcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGAt                    <  1:2489382/54‑1 (MQ=255)
                                                                    tcGAATATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAAt  >  1:2191541/1‑71 (MQ=255)
                                                                    tcGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGAt          <  1:2928213/63‑1 (MQ=255)
                                                                     cGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAg      >  1:3270839/1‑66 (MQ=255)
                                                                      |                                                                    
GCGGAGAAACTTCTGCCGGATATTCAGTAATGAAGGTCGGCTGAATCAGATGTGCTTCTGCCACTTCTTCGAAGATCTCGGTAACGATACGGCCCAGACCCCAGCTCTTCTCAACGTGGATGCCGATAGATTCAGCAAT  >  minE/1933245‑1933383

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