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
A2 F28 I1 R1 155 60.3 2039550 99.3% 2025273 138.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,462,889 (C)9→8 intergenic (+243/‑123) fadL → / → yfdF long‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,462,8810C.97.7% 175.2 / ‑1.9 43intergenic (+235/‑131)fadL/yfdFlong‑chain fatty acid outer membrane channel/bacteriophage T2 receptor/protein YfdF
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base . (13/29);  total (13/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.95e-01

TTTGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTCCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATC  >  NC_000913/2462742‑2463011
                                                                                                                                           |                                                                                                                                  
tttGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTc                                                                                                                                    <  2:896549/140‑1 (MQ=255)
 ttGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcc                                                                                                                                   <  1:411435/140‑1 (MQ=255)
   gCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccc                                                                                                                                 <  1:311784/140‑1 (MQ=255)
     aaaCAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccc                                                                                                                               <  1:821703/140‑1 (MQ=255)
           ccTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTcccccccctggc                                                                                                                         >  2:998058/1‑136 (MQ=255)
                tGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATtg                                                                                                                   <  1:204900/140‑1 (MQ=255)
                tGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATtg                                                                                                                   <  2:456936/140‑1 (MQ=255)
                  gCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATtgtg                                                                                                                 <  1:1003395/140‑1 (MQ=255)
                  gCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATtgtg                                                                                                                 <  1:476957/140‑1 (MQ=255)
                   cAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTgc                                                                                                                <  2:678266/140‑1 (MQ=255)
                    aGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTgcg                                                                                                               <  2:964767/140‑1 (MQ=255)
                            cTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATaca                                                                                                       <  2:48346/140‑1 (MQ=255)
                               tCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTCCCCCCCCCTGGCTATTGTGCGCTCATACACt                                                                                                     <  2:983020/140‑1 (MQ=255)
                               tCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTc                                                                                                    <  1:919014/140‑1 (MQ=255)
                               tCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTc                                                                                                    <  1:58739/140‑1 (MQ=255)
                                          aGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGAt                                                                                         <  2:204702/140‑1 (MQ=255)
                                               tATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGtt                                                                                    <  2:274911/140‑1 (MQ=255)
                                                aTCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTc                                                                                   >  1:23454/1‑140 (MQ=255)
                                                  ccACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCta                                                                                 >  1:815381/1‑140 (MQ=255)
                                                      aGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCtaaata                                                                             >  2:648822/1‑140 (MQ=255)
                                                            aCCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAg                                                                       <  1:648822/140‑1 (MQ=255)
                                                            aCCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAg                                                                       <  2:896848/140‑1 (MQ=255)
                                                             ccTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGc                                                                      >  1:806848/1‑140 (MQ=255)
                                                                gAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGtt                                                                   >  2:472857/1‑140 (MQ=255)
                                                                      aaaGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGa                                                             <  1:453580/140‑1 (MQ=255)
                                                                      aaaGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCACACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGa                                                             <  1:190760/140‑1 (MQ=255)
                                                                        aGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATa                                                           <  2:27710/140‑1 (MQ=255)
                                                                             tatTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTGTTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTa                                                      <  2:699735/140‑1 (MQ=255)
                                                                             tatTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTa                                                      <  2:806848/140‑1 (MQ=255)
                                                                                    aGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATTAATGAGCGTTTTTTGATAGTCTATTTCAtt                                               <  1:964944/140‑1 (MQ=255)
                                                                                    aGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTa                                                      <  1:60398/133‑1 (MQ=255)
                                                                                    aGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTa                                                      >  2:60398/1‑133 (MQ=255)
                                                                                    aGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCAtt                                               <  1:728573/140‑1 (MQ=255)
                                                                                         ttCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAg                                             <  2:187062/137‑1 (MQ=255)
                                                                                         ttCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAg                                             >  1:187062/1‑137 (MQ=255)
                                                                                           cTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTa                                                      <  2:719772/126‑1 (MQ=255)
                                                                                           cTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTa                                                      >  1:719772/1‑126 (MQ=255)
                                                                                             gCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAatat                                      <  2:812451/140‑1 (MQ=255)
                                                                                                 gTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAatatatat                                  <  1:157812/140‑1 (MQ=255)
                                                                                                   ccTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCAtt                                               >  2:719075/1‑125 (MQ=255)
                                                                                                   ccTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCAtt                                               <  1:719075/125‑1 (MQ=255)
                                                                                                   ccTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATAttt                                >  1:269734/1‑140 (MQ=255)
                                                                                                                tttACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAaatcaat                   <  2:224665/140‑1 (MQ=255)
                                                                                                                tttACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAaatcaat                   <  2:815381/140‑1 (MQ=255)
                                                                                                                  tACTTTTCTGCATTTCCAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAatcaatca                 >  2:482350/1‑140 (MQ=255)
                                                                                                                                 ccAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATc  <  1:722658/140‑1 (MQ=255)
                                                                                                                                 ccAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATc  >  2:722658/1‑140 (MQ=255)
                                                                                                                                 ccAGGATACT‑CCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATc  >  1:473962/1‑140 (MQ=255)
                                                                                                                                           |                                                                                                                                  
TTTGCAAACAGCCTGTTGGCAGCTTGCCCTTTCAAATCAATAAGCGGTATCCACAGACAAACCTGAAGGGAAAGGCATATTTTCAGGCGTTCTGCTCGTCCTTCTCAAAGAGTTTACTTTTCTGCATTTCCAGGATACTCCCCCCCCCTGGCTATTGTGCGCTCATACACTCAAATTAAAGATAGGTTCTAAATAAATGAGCGTTTTTTGATAGTCTATTTCATTAGGTAATATATATTTGTAACAAATCAATCAAAATGGAATAAAATC  >  NC_000913/2462742‑2463011

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