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
A4 F1 I2 R1 780 68.3 3343050 93.5% 3125751 102.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 515,808 C→T intergenic (‑35/‑111) qmcA ← / → fetA PHB domain membrane‑anchored putative protease/iron export ABC transporter ATPase, peroxide resistance protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913515,8080CT100.0% 192.6 / NA 60intergenic (‑35/‑111)qmcA/fetAPHB domain membrane‑anchored putative protease/iron export ABC transporter ATPase, peroxide resistance protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (30/30);  total (30/30)

CCACTGATAGCCCTGCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGCAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGATGCAGGAAAATAGTCC  >  NC_000913/515687‑515935
                                                                                                                         |                                                                                                                               
ccACTGATAGCCCTGCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGAtt                                                                                                                <  2:1445029/139‑1 (MQ=255)
   cTGATAGCCCTGCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             <  1:1533012/139‑1 (MQ=255)
                  tACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                              >  2:314744/1‑139 (MQ=255)
                    cGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             >  1:78108/1‑122 (MQ=255)
                    cGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             <  2:78108/122‑1 (MQ=255)
                     gATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGTATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAGTAc                                                                                           <  1:1077426/139‑1 (MQ=255)
                       ttttGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTg                                                                                         >  1:302667/1‑139 (MQ=255)
                                ccGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGt                                                                                <  2:302667/139‑1 (MQ=255)
                                ccGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGt                                                                                <  1:314744/139‑1 (MQ=255)
                                 cgcgCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             <  1:517238/109‑1 (MQ=255)
                                 cgcgCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             >  2:517238/1‑109 (MQ=255)
                                        aCAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCtt                                                                        >  2:1323900/1‑139 (MQ=255)
                                            tGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTc                                                                    <  1:1323900/139‑1 (MQ=255)
                                                  gcgcGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             >  2:802078/1‑92 (MQ=255)
                                                  gcgcGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             <  1:802078/92‑1 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGGTAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             <  2:1496305/91‑1 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAAt                                                                                                                            <  2:796306/76‑1 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAAt                                                                                                                            >  1:796306/1‑76 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             <  1:1420314/91‑1 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             <  1:418304/91‑1 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             >  2:418304/1‑91 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             >  1:488530/1‑91 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             >  2:1420314/1‑91 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             <  2:488530/91‑1 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                             >  1:1496305/1‑91 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                              >  2:613572/1‑106 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                              <  1:613572/106‑1 (MQ=255)
                                                   cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGaa                                                             >  1:886731/1‑139 (MQ=255)
                                                        cAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                              <  1:716893/101‑1 (MQ=255)
                                                        cAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                              >  2:716893/1‑101 (MQ=255)
                                                        cAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATa                                                        >  1:95205/1‑139 (MQ=255)
                                                         aaaaaTGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATta                                                                                                      >  1:390564/1‑92 (MQ=255)
                                                         aaaaaTGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATta                                                                                                      <  2:390564/92‑1 (MQ=255)
                                                                  aaTCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                              >  2:1569367/1‑91 (MQ=255)
                                                                  aaTCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                              <  1:1569367/91‑1 (MQ=255)
                                                                                  aGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACaaa                                                                                                         <  2:1142809/64‑1 (MQ=255)
                                                                                  aGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACaaa                                                                                                         >  1:1142809/1‑64 (MQ=255)
                                                                                  aGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGaaaa                              >  1:179029/1‑139 (MQ=255)
                                                                                   gCATCGGAAAATCCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGaaaaa                             <  2:95205/139‑1 (MQ=255)
                                                                                        ggAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTc                                                                    <  2:896415/95‑1 (MQ=255)
                                                                                        ggAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTc                                                                    >  1:896415/1‑95 (MQ=255)
                                                                                         gAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGtt                                                                               >  1:1201714/1‑83 (MQ=255)
                                                                                         gAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGtt                                                                               <  2:1201714/83‑1 (MQ=255)
                                                                                         gAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAAc                       >  1:1365576/1‑139 (MQ=255)
                                                                                         gAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAAc                       >  1:432819/1‑139 (MQ=255)
                                                                                              aCCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATaaa                                                      >  2:1102930/1‑103 (MQ=255)
                                                                                              aCCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATaaa                                                      >  2:802507/1‑103 (MQ=255)
                                                                                              aCCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATaaa                                                      <  1:802507/103‑1 (MQ=255)
                                                                                              aCCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGACTAAACAAATTATACCTGATAACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATaaa                                                      <  1:1102930/103‑1 (MQ=255)
                                                                                                    tgttgtACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGa                  <  2:224146/133‑1 (MQ=255)
                                                                                                    tgttgtACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGa                  >  1:224146/1‑133 (MQ=255)
                                                                                                              tCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                              >  2:755636/1‑47 (MQ=255)
                                                                                                              tCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                              <  1:1441840/47‑1 (MQ=255)
                                                                                                              tCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                              <  1:755636/47‑1 (MQ=255)
                                                                                                              tCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                              >  2:1441840/1‑47 (MQ=255)
                                                                                                              tCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCg                                                               >  1:415454/1‑78 (MQ=255)
                                                                                                              tCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCg                                                               <  2:415454/78‑1 (MQ=255)
                                                                                                              tCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGATGCAGGAAAATAGTcc  <  2:886731/139‑1 (MQ=255)
                                                                                                                   aaTCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGa                  >  1:1498293/1‑118 (MQ=255)
                                                                                                                   aaTCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGa                  <  2:1498293/118‑1 (MQ=255)
                                                                                                                         |                                                                                                                               
CCACTGATAGCCCTGCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGCAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGATGCAGGAAAATAGTCC  >  NC_000913/515687‑515935

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A