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
A7 F1 I2 R1 766 64.2 3232166 90.9% 2938038 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,806,042 (C)6→7 coding (42/759 nt) ydiY ← acid‑inducible putative outer membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,806,0361.C100.0% 137.7 / NA 40G16G (GGC→GGG) ydiYacid‑inducible putative outer membrane protein
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (17/23);  total (17/23)

CTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGAAA  >  NC_000913/1805905‑1806167
                                                                                                                                    |                                                                                                                                   
cTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑ccccccc                                                                                                                              >  1:286609/1‑138 (MQ=255)
 ttttCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccccccg                                                                                                                             >  2:529315/1‑137 (MQ=255)
  tttCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccccccgc                                                                                                                            <  1:1375153/139‑4 (MQ=255)
  tttCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccccccgc                                                                                                                            <  1:530580/139‑4 (MQ=255)
          tGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATaa                                                                                                                     >  1:144003/1‑139 (MQ=255)
          tGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cc                                                                                                                                   <  1:276436/124‑1 (MQ=255)
          tGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cc                                                                                                                                   >  2:276436/1‑124 (MQ=255)
                   gtgCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAg                                                                                                            >  1:1378271/1‑139 (MQ=255)
                    tgCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAgg                                                                                                           >  1:729573/1‑139 (MQ=255)
                      cAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGaa                                                                                                         <  2:729573/139‑1 (MQ=255)
                      cAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGaa                                                                                                         <  2:144003/139‑1 (MQ=255)
                            atCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCt                                                                                                   >  1:1433530/1‑139 (MQ=255)
                                 gCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCaaa                                                                                              <  1:5072/139‑1 (MQ=255)
                                  cGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAATACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccc                                                                                                                                 <  1:33632/102‑1 (MQ=255)
                                  cGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccc                                                                                                                                 >  2:33632/1‑102 (MQ=255)
                                   gTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAg                                                                                            >  2:978158/1‑139 (MQ=255)
                                   gTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccccccgc                                                                                                                            <  2:1081679/106‑4 (MQ=255)
                                   gTTCAGATTACCTACGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccccccgc                                                                                                                            >  1:1081679/1‑103 (MQ=255)
                                     tCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cc                                                                                                                                   <  2:1466967/97‑1 (MQ=255)
                                     tCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cc                                                                                                                                   >  1:1466967/1‑97 (MQ=255)
                                        gATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCa                                                                                       <  2:286609/139‑1 (MQ=255)
                                        gATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCa                                                                                       <  2:1433530/139‑1 (MQ=255)
                                               ttCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCCTTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCa                                                                                <  1:238684/139‑1 (MQ=255)
                                               ttCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCa                                                                                <  1:1385599/139‑1 (MQ=255)
                                               ttCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCa                                                                                <  1:529315/139‑1 (MQ=255)
                                               ttCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCa                                                                                <  1:978158/139‑1 (MQ=255)
                                               ttCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCa                                                                                <  2:1378271/139‑1 (MQ=255)
                                                   aaaGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACg                                                                                                                   >  1:1604868/1‑100 (MQ=255)
                                                   aaaGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACg                                                                                                                   <  2:1604868/100‑1 (MQ=255)
                                                    aaGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGt                                                                           <  2:420702/139‑1 (MQ=255)
                                                       gTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCg                                                                        >  1:1114685/1‑139 (MQ=255)
                                                        ttttttAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGt                                                                       <  2:820163/139‑1 (MQ=255)
                                                         tttttAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTa                                                                      >  2:1413026/1‑139 (MQ=255)
                                                          ttttAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTac                                                                     <  1:1413026/139‑1 (MQ=255)
                                                                  cTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACaaaaa                                                             >  2:346171/1‑139 (MQ=255)
                                                                               ccATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑ccccccc                                                                                                                              >  2:1275350/1‑59 (MQ=255)
                                                                               ccATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑ccccccc                                                                                                                              <  1:1275350/60‑2 (MQ=255)
                                                                                  tGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGt                                             <  2:1114685/139‑1 (MQ=255)
                                                                                    aCAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGaa                                                                                                         >  1:1482291/1‑77 (MQ=255)
                                                                                    aCAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGaa                                                                                                         <  2:1482291/77‑1 (MQ=255)
                                                                                     cAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccc                                                                                                                                 <  2:1520922/51‑1 (MQ=255)
                                                                                     cAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑cccc                                                                                                                                 >  1:1520922/1‑51 (MQ=255)
                                                                                        tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACg                                                                                                                   >  1:967677/1‑63 (MQ=255)
                                                                                        tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACg                                                                                                                   <  2:967677/63‑1 (MQ=255)
                                                                                        tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGa                                       >  2:1036336/1‑139 (MQ=255)
                                                                                        tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGa                                       >  1:1116839/1‑139 (MQ=255)
                                                                                        tAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGa                                       >  1:1566822/1‑139 (MQ=255)
                                                                                                  atcatcGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAAGTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTa                             <  1:1036336/139‑1 (MQ=255)
                                                                                                      tcGGCAGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGa                         <  2:1116839/139‑1 (MQ=255)
                                                                                                           aGCTGCATTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCaaa                    >  2:1405094/1‑139 (MQ=255)
                                                                                                                 aTTCAGTGACGCAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGATACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAg              <  1:209653/139‑1 (MQ=255)
                                                                                                                            cAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCt       >  2:921141/1‑135 (MQ=255)
                                                                                                                            cAAACATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGAGCAAAGATTAGCGTCCCt       <  1:921141/135‑1 (MQ=255)
                                                                                                                             aaaCATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGaaa  <  1:1405094/139‑1 (MQ=255)
                                                                                                                               aCATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGaa                                      <  2:485090/101‑1 (MQ=255)
                                                                                                                               aCATGCCCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGaa                                      >  1:485090/1‑101 (MQ=255)
                                                                                                                                    |                                                                                                                                   
CTTTTCGTATTGCCTGATTGTGCAAGATATCCTGCGTTCAGATTACCTTCGAAAGGTTTTTTAGCGCTGGCAGGATCATCCATGACAGTAAAAACGGAATCATCGGCAGCTGCATTCAGTGACGCAAACATG‑CCCCCCGCCAACATAACGATGGCAGGAACTGTCTTCAAAAGCTTCATTTATCAAGAGTCCGTACAACAAAAAAAGAGACCATCGCGGTCCCGGAAACTTTCTTAAGGATCAAAGATTAGCGTCCCTGGAAA  >  NC_000913/1805905‑1806167

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A