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 F28 I1 R1 260 73.5 2514320 99.3% 2496719 138.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,705,117 C→T A65T (GCT→ACT)  lepB ← signal peptidase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,705,1170CT96.3% 171.0 / ‑2.1 54A65T (GCT→ACT) lepBsignal peptidase I
Reads supporting (aligned to +/- strand):  ref base C (2/0);  new base T (31/21);  total (33/21)
Fisher's exact test for biased strand distribution p-value = 5.16e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.66e-01

GCCATAAGCAAACTTCTCTACCAGAATAAAATCACCAATTAACAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGCACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTGCGAAAAAGAATTTATCCACGCA  >  NC_000913/2704980‑2705249
                                                                                                                                         |                                                                                                                                    
gCCATAAGCAAACTTCTCTACCAGAATAAAATCACCAATTAACAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTAc                                                                                                                                    >  2:1078294/1‑140 (MQ=255)
    tAAGCAAACTTCTCTACCAGAATAAAATCACCAATTAACAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTGCCGGAAAAACAGAAGTACCGGt                                                                                                                                >  2:602655/1‑140 (MQ=255)
    tAAGCAAACTTCTCTACCAGAATAAAATCACCAATTAACAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGt                                                                                                                                >  1:1118528/1‑140 (MQ=255)
                 ctACCAGAATAAAATCACCAATTAACAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGCACCGGAAAAACAGAAGTACCGGTTTccagccagcca                                                                                                                   >  2:451055/1‑140 (MQ=255)
                      aGAATAAAATCACCAATTAACAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCtt                                                                                                              <  1:1044689/140‑1 (MQ=255)
                         aTAAAATCACCAATTAACAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCgg                                                                                                           >  1:482573/1‑140 (MQ=255)
                         aTAAAATCACCAATTAAAAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCgg                                                                                                           >  1:711698/1‑140 (MQ=255)
                           aaaaTCACCAATTAACAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGgcg                                                                                                         <  2:1248558/140‑1 (MQ=255)
                           aaaaTCACCAATTAACAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGgcg                                                                                                         <  1:953970/140‑1 (MQ=255)
                             aaTCACCAATTAAAAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCa                                                                                                       <  2:711698/140‑1 (MQ=255)
                                          cAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGCACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACg                                                                                          <  1:451055/140‑1 (MQ=255)
                                           agagTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGt                                                                                         >  2:28415/1‑140 (MQ=255)
                                             agTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTg                                                                                       >  1:1252816/1‑140 (MQ=255)
                                             agTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTg                                                                                       >  2:551752/1‑140 (MQ=255)
                                             agTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTg                                                                                       >  1:202061/1‑140 (MQ=255)
                                              gTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGc                                                                                      <  2:18598/140‑1 (MQ=255)
                                               tCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCt                                                                                     >  2:164085/1‑140 (MQ=255)
                                               tCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCt                                                                                     <  2:896167/140‑1 (MQ=255)
                                               tCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCt                                                                                     <  1:1162142/140‑1 (MQ=255)
                                                 ggCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCttt                                                                                   >  1:629509/1‑140 (MQ=255)
                                                   catcatCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTAt                                                                                 >  2:860691/1‑140 (MQ=255)
                                                    atcatcGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATc                                                                                >  2:339190/1‑140 (MQ=255)
                                                       atcGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAg                                                                             >  1:79089/1‑140 (MQ=255)
                                                        tcGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGt                                                                            <  1:1087562/140‑1 (MQ=255)
                                                        tcGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGt                                                                            <  1:339190/140‑1 (MQ=255)
                                                         cGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTg                                                                           >  1:420994/1‑140 (MQ=255)
                                                               tGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTccc                                                                     <  1:164085/140‑1 (MQ=255)
                                                               tGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTccc                                                                     <  2:420994/140‑1 (MQ=255)
                                                                gACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTcccc                                                                    >  2:236063/1‑140 (MQ=255)
                                                                    ggATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCa                                                                <  1:979145/140‑1 (MQ=255)
                                                                     gATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAg                                                               <  2:202061/140‑1 (MQ=255)
                                                                               ggTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTgcgc                                                     <  1:860691/140‑1 (MQ=255)
                                                                                gTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTGCCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGcgcc                                                    <  1:602655/140‑1 (MQ=255)
                                                                                gTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGcgcc                                                    >  2:608113/1‑140 (MQ=255)
                                                                                gTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGcgcc                                                    <  1:28415/140‑1 (MQ=255)
                                                                                 ttCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGcgccg                                                   >  2:441855/1‑140 (MQ=255)
                                                                                   cATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCt                                                 >  1:461634/1‑140 (MQ=255)
                                                                                     taaataaaCGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGc                                               <  1:551752/140‑1 (MQ=255)
                                                                                       aataaaCGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCACCCTTTTTCAACGTTGTTTTATCCGGTGAGCCCCCGGCAGCCGCCTGCGCCGCTGCCt                                             <  2:503987/140‑1 (MQ=255)
                                                                                           aacgaacgCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACg                                         >  1:968776/1‑140 (MQ=255)
                                                                                           aacgaacgCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACg                                         >  1:946901/1‑140 (MQ=255)
                                                                                           aacgaacgCACAATCAATACGAGAGCCAGTACCGGAAAAACAGAAGCACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGGGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACg                                         >  2:1035949/1‑140 (MQ=255)
                                                                                               aacgCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGTTTTATCCAGTGAGCCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTcc                                     <  2:1252816/140‑1 (MQ=255)
                                                                                                            tACGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTg                        >  2:370245/1‑140 (MQ=255)
                                                                                                              cGATAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTGCg                      >  2:879491/1‑140 (MQ=255)
                                                                                                                aTAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTGCGaa                    >  2:852860/1‑140 (MQ=255)
                                                                                                                aTAGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTGCGaa                    >  2:345735/1‑140 (MQ=255)
                                                                                                                aTAGCCAGTACCGGAAAAACAGAAGCACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTGCGaa                    >  1:292342/1‑140 (MQ=255)
                                                                                                                  aGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAGCGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGttt                             >  2:1219785/1‑129 (MQ=255)
                                                                                                                  aGCCAGTACCGGAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAGCGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGttt                             <  1:1219785/129‑1 (MQ=255)
                                                                                                                             gtaaaaCAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTGCGAAAAAGAATTTATcc       >  1:562954/3‑140 (MQ=255)
                                                                                                                             gAAAAACAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTGCGAAAAAGAATTTATcc       >  1:772660/1‑140 (MQ=255)
                                                                                                                                aaaCAGAAGTCCCGGTTTCCAGCCAGCCAGGCTTCGGCGCACCCTTTTTCAACGTTGCTTTATCCAGTGAGCCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTGCGAAAAAGAATTTATCCACg    <  1:254787/140‑1 (MQ=255)
                                                                                                                                 aaCAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTGCGAAAAAGAATTTATCCACGc   >  2:81410/1‑140 (MQ=255)
                                                                                                                                 aaCAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTGCGAAAAAGAATTTATCCACGc   <  1:192299/140‑1 (MQ=255)
                                                                                                                                  aCAGAAGTACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTGCGAAAAAGAATTTATCCACGCa  >  1:1025410/1‑140 (MQ=255)
                                                                                                                                         |                                                                                                                                    
GCCATAAGCAAACTTCTCTACCAGAATAAAATCACCAATTAACAGAGTCGGCATCATCGAACCTGACGGGATCTGGAACGGTTCATAAATAAACGAACGCACAATCAATACGATAGCCAGTACCGGAAAAACAGAAGCACCGGTTTCCAGCCAGCCAGGCTTCGGCGCAACCTTTTTCAACGTTGCTTTATCCAGTGAGTCCCCGGCAGCCGCCTGCGCCGCTGCCTGACGTTCCCGCCGTTTAGGTGCGAAAAAGAATTTATCCACGCA  >  NC_000913/2704980‑2705249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A