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
A9 F1 I1 R1 759 71.0 3673240 91.5% 3361014 104.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,002,813 C→T *127* (TAG→TAA)  yigG ← PRK11371 family inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,002,8130CT100.0% 185.7 / NA 58*127* (TAG→TAA) yigGPRK11371 family inner membrane protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (31/27);  total (31/27)

TTTATATTCTGGTGTTGCCCCCCAGAATCCAGGAAAACCATGTTGATCATAAAAATTAAATCGGTATTTCCATTTTTCACTTAATGAACCATCGTTCATATATTCCTTACTCATAAATACTCCATAACTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATAGAGATGATAT  >  NC_000913/4002686‑4002946
                                                                                                                               |                                                                                                                                     
tttATATTCTGGTGTTGCCCCCCAGAATCCAGGAAAACCATGTTGATCATAAAAATTAAATCGGTATTTCCATTTTTCACTTAATGAACCATCGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTtga                                                                                                                            <  1:796886/139‑1 (MQ=255)
 ttATATTCTGGTGTTGCCCCCCAGAATCCAGGAAAACCATGTTGATCATAAAAATTAAATCGGTATTTCCATTTTTCACTTAATGAACCATCGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTtgat                                                                                                                           <  2:193367/139‑1 (MQ=255)
         tGGTGTTGCCCCCCAGAATCCAGGAAAACCATGTTGATCATAAAAATTAAATCGGTATTTCCATTTTTCACTTAATGAACCATCGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGt                                                                                                                   >  1:834859/1‑139 (MQ=255)
           gtgtTGCCCCCCAGAATCCAGGAAAACCATGTTGATCATAAAAATTAAATCGGTATTTCCATTTTTCACTTAATGAACAATCGTTCATATATTCCTTACTCATAAATACTCTATAATTATTGTTTTTATGAATCAGTAg                                                                                                                 >  2:113896/1‑139 (MQ=255)
                gCCCCCCAGAATCCAGGAAAACCATGTTGATCATAAAAATTAAATCGGTATTTCCATTTTTCACTTAATGAACCATCGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCa                                                                                                            <  2:96430/139‑1 (MQ=255)
                  cccccAGAATCCAGGAAAACCATGTTGATCATAAAAATTAAATCGGTATTTCCATTTTTCACTTAATGAACCATCGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAg                                                                                                          <  2:1059189/139‑1 (MQ=255)
                    cccAGAATCCAGGAAAACCATGTTGATCATAAAAATTAAATCGGTATTTCCATTTTTCACTTAATGAACCATCGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCa                                                                                                        <  1:1595219/139‑1 (MQ=255)
                            ccAGGAAAACCATGTTGATCATAAAAATTAAATCGGTATTTCCATTTTTCACTTAATGAACCATCGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATa                                                                                                <  1:113896/139‑1 (MQ=255)
                                                                                ttAATGAACCATCGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGt                                                                                                                   >  2:304498/1‑68 (MQ=255)
                                                                                ttAATGAACCATCGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGt                                                                                                                   <  1:304498/68‑1 (MQ=255)
                                                                                          aTCGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATc                                  >  2:1368391/1‑139 (MQ=255)
                                                                                          aTCGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATc                                  >  1:1753637/1‑139 (MQ=255)
                                                                                            cGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGt                                                                                                                                 <  1:443926/42‑1 (MQ=255)
                                                                                            cGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGt                                                                                                                                 >  2:443926/1‑42 (MQ=255)
                                                                                            cGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCa                                                                                                            <  1:76308/63‑1 (MQ=255)
                                                                                            cGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCa                                                                                                            >  2:76308/1‑63 (MQ=255)
                                                                                            cGTTCATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCtt                                >  2:136546/1‑139 (MQ=255)
                                                                                                cATATATTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGc                            <  1:136546/139‑1 (MQ=255)
                                                                                                   atatTCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTAt                         >  1:1561794/1‑139 (MQ=255)
                                                                                                      ttCCTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCAt                      <  1:1373457/139‑1 (MQ=255)
                                                                                                         cTTACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATtgt                   >  2:40520/1‑139 (MQ=255)
                                                                                                          ttACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATtgtg                  >  2:851364/1‑139 (MQ=255)
                                                                                                           tACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCACACATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGTACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTgaga                 >  1:80942/1‑139 (MQ=255)
                                                                                                           tACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGa                                                                                     >  2:874205/1‑71 (MQ=255)
                                                                                                           tACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGa                                                                                     <  1:874205/71‑1 (MQ=255)
                                                                                                           tACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCg                                                           <  1:229202/97‑1 (MQ=255)
                                                                                                           tACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCg                                                           >  2:229202/1‑97 (MQ=255)
                                                                                                           tACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGtga                 >  2:1829559/1‑139 (MQ=255)
                                                                                                           tACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGtga                 <  2:1561794/139‑1 (MQ=255)
                                                                                                           tACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGtga                 <  1:1035495/139‑1 (MQ=255)
                                                                                                           tACTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGtga                 >  2:1035495/1‑139 (MQ=255)
                                                                                                            aCTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCgg                             <  1:305051/126‑1 (MQ=255)
                                                                                                            aCTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCgg                             >  2:305051/1‑126 (MQ=255)
                                                                                                            aCTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGtgat                >  2:1601324/1‑139 (MQ=255)
                                                                                                             cTCATAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGtgatg               >  1:1528259/1‑139 (MQ=255)
                                                                                                                aTAAATACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATa            >  1:414726/1‑139 (MQ=255)
                                                                                                                  aaaTACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATaga          >  1:1797182/1‑139 (MQ=255)
                                                                                                                   aaTACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATagag         <  2:1528259/139‑1 (MQ=255)
                                                                                                                   aaTACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATagag         <  2:414726/139‑1 (MQ=255)
                                                                                                                   aaTACTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATagag         <  1:40520/139‑1 (MQ=255)
                                                                                                                       cTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATC‑AAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATagag         >  1:1183052/1‑134 (MQ=255)
                                                                                                                       cTCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATC‑AAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATagag         <  2:1183052/134‑1 (MQ=255)
                                                                                                                        tCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATtgt                   <  1:1676509/124‑1 (MQ=255)
                                                                                                                        tCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATtgt                   >  2:1676509/1‑124 (MQ=255)
                                                                                                                        tCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATagag         >  1:639396/1‑134 (MQ=255)
                                                                                                                        tCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATagag         <  2:639396/134‑1 (MQ=255)
                                                                                                                        tCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATAGAgatgat    >  1:120870/1‑139 (MQ=255)
                                                                                                                        tCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATAGAgatgat    <  1:1368391/139‑1 (MQ=255)
                                                                                                                        tCCATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATAGAgatgat    >  1:761085/1‑139 (MQ=255)
                                                                                                                          cATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTc                               >  2:1236589/1‑110 (MQ=255)
                                                                                                                          cATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTc                               <  1:1236589/110‑1 (MQ=255)
                                                                                                                          cATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATagag         >  1:194256/1‑132 (MQ=255)
                                                                                                                          cATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATagag         <  2:194256/132‑1 (MQ=255)
                                                                                                                          cATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATa            <  2:1583802/129‑1 (MQ=255)
                                                                                                                          cATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATa            >  1:1583802/1‑129 (MQ=255)
                                                                                                                          cATAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATAGAGATGatat  >  2:953739/1‑139 (MQ=255)
                                                                                                                            tAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATaa                                                                              >  2:911739/1‑61 (MQ=255)
                                                                                                                            tAATTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATagag         <  2:480436/130‑1 (MQ=255)
                                                                                                                               |                                                                                                                                     
TTTATATTCTGGTGTTGCCCCCCAGAATCCAGGAAAACCATGTTGATCATAAAAATTAAATCGGTATTTCCATTTTTCACTTAATGAACCATCGTTCATATATTCCTTACTCATAAATACTCCATAACTATTGTTTTGATGAATCAGTAGGTGCAAGCATTAGCATACTGAAAGTGGAAAAATAACAAATCAAAAAAATCATCGAACCATTGCCTGAACAGGCAAAATCTTCGGCTATCATTGTGATGATAGAGATGATAT  >  NC_000913/4002686‑4002946

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ 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