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 F28 I1 R1 163 52.9 1786516 99.3% 1774010 139.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,976,679 T→C H154R (CAC→CGC)  motA ← motility protein A

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,976,6790TC97.4% 126.6 / ‑4.5 38H154R (CAC→CGC) motAmotility protein A
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base C (16/21);  total (17/21)
Fisher's exact test for biased strand distribution p-value = 4.47e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGTGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAGGATGCGTGGGTAGCTGGCGAA  >  NC_000913/1976543‑1976812
                                                                                                                                        |                                                                                                                                     
aCCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTcgcgcg                                                                                                                                    >  1:39651/1‑140 (MQ=255)
aCCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTcgcgcg                                                                                                                                    >  2:103410/1‑140 (MQ=255)
     gCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGGCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCa                                                                                                                               >  1:442086/1‑140 (MQ=255)
     gCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCa                                                                                                                               <  1:285495/140‑1 (MQ=255)
     gCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCa                                                                                                                               <  2:1413/140‑1 (MQ=255)
           cggcAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATctct                                                                                                                         <  1:267862/140‑1 (MQ=255)
           cggcAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATctct                                                                                                                         <  2:27225/140‑1 (MQ=255)
                ggACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTcatc                                                                                                                    >  1:133230/1‑140 (MQ=255)
                      tCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCag                                                                                                              <  1:103410/140‑1 (MQ=255)
                                    cgcgTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGa                                                                                                <  2:844385/140‑1 (MQ=255)
                                      cgTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAg                                                                                              <  2:79720/140‑1 (MQ=255)
                                      cgTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAg                                                                                              <  2:364747/140‑1 (MQ=255)
                                           aCGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGtt                                                                                         <  2:686653/140‑1 (MQ=255)
                                             gACCCCCATTACAGGCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCa                                                                                       <  2:442086/140‑1 (MQ=255)
                                               cccccATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCAtg                                                                                     >  1:517570/1‑140 (MQ=255)
                                                      tACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGc                                                                              <  2:39651/140‑1 (MQ=255)
                                                      tACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGc                                                                              <  2:81074/140‑1 (MQ=255)
                                                         aGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGCAGGTGTTCATGTGACCGCTGa                                                                           <  2:632918/140‑1 (MQ=255)
                                                                     aCCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCa                                                               <  1:882253/140‑1 (MQ=255)
                                                                       cAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGa                                                             >  2:6219/1‑140 (MQ=255)
                                                                            gCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATc                                                        >  2:184337/1‑140 (MQ=255)
                                                                              cGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATcga                                                      >  1:573466/1‑140 (MQ=255)
                                                                                          cccGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCaa                                          >  1:723454/1‑140 (MQ=255)
                                                                                                   cgcCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGc                                 >  2:562664/1‑140 (MQ=255)
                                                                                                         aCTGTTCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCcg                           >  2:355776/1‑140 (MQ=255)
                                                                                                             ttCGCCGGGACTTCTGCCTCGCTTTCGTGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAg                       >  2:192974/1‑140 (MQ=255)
                                                                                                             ttCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAg                       >  2:696655/1‑140 (MQ=255)
                                                                                                             ttCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAg                       >  2:395431/1‑140 (MQ=255)
                                                                                                             ttCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAg                       <  1:6219/140‑1 (MQ=255)
                                                                                                              tCGCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAgg                      <  2:517570/140‑1 (MQ=255)
                                                                                                                gCCGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGTTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAGGAt                    >  1:421320/1‑140 (MQ=255)
                                                                                                                  cGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCGTGACGCTATCCGCGAg                       >  2:812667/1‑135 (MQ=255)
                                                                                                                  cGGGACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAg                       <  1:812667/135‑1 (MQ=255)
                                                                                                                     gACTTCTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAGGATGCGTg               >  1:57117/1‑140 (MQ=255)
                                                                                                                          cTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGTTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAGGATGCGTGGGTAg          <  2:421320/140‑1 (MQ=255)
                                                                                                                          cTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAGGATGCGTGGGTAg          <  2:57117/140‑1 (MQ=255)
                                                                                                                          cTGCCTCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAGGATGCGTGGGTAg          <  1:562664/140‑1 (MQ=255)
                                                                                                                               tCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAGGATGCGTGGGTAGCTGGc     <  2:573466/140‑1 (MQ=255)
                                                                                                                               tCGCTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAGGATGCGTGGGTAGCTGGc     >  2:334864/1‑140 (MQ=255)
                                                                                                                                  cTTTCGCGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAGGATGCGTGGGTAGCTGGCGaa  >  2:764673/1‑140 (MQ=255)
                                                                                                                                        |                                                                                                                                     
ACCCAGCTCGGCGGCAGGACGATCGGCTGAACCTAACGCGTGAACGACCCCCATTACAGCCGCAACAATACCAAACGCCGGAAGTGAGTCCCCGACCAGCGCCAGACTGTTCGCCGGGACTTCTGCCTCGCTTTCGTGCGTCTCAATCTCTTCATCCATCAGAGCTTCGATTTCGAAGGTGTTCATGTGACCGCTGATAATCAGGCGCAGATAATCGACGATAAAATCAAGCATGACGCTATCCGCGAGGATGCGTGGGTAGCTGGCGAA  >  NC_000913/1976543‑1976812

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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