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
A8 F1 I2 R1 765 53.2 2691310 93.4% 2513683 103.8

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% 177.5 / NA 55intergenic (‑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 (26/29);  total (26/29)

CTACTGTCCACTGATAGCCCTGCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGCAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGATGCAGGAAAATAGTCCTT  >  NC_000913/515680‑515937
                                                                                                                                |                                                                                                                                 
cTACTGTCCACTGATAGCCCTGCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATtgctg                                                                                                                         >  2:972661/1‑139 (MQ=255)
    tatCCACTGATAGCCCTGCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTg                                                                                                                     >  1:546432/3‑139 (MQ=255)
      tCCACTGATAGCCCTGCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGAt                                                                                                                   >  1:543471/1‑139 (MQ=255)
        cACTGATAGCCCTGCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTa                                                                                                                 >  1:744913/1‑139 (MQ=255)
          cTGATAGCCCTGCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                               <  1:930126/139‑1 (MQ=255)
           tGATAGCCCTGCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAAc                                                                                                              >  1:982084/1‑139 (MQ=255)
                   cTGCGGTACGATTTTGACACCCGCGCGGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATtata                                                                                                      <  1:581339/139‑1 (MQ=255)
                     gCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATAcc                                                                                                    >  1:1267753/1‑139 (MQ=255)
                     gCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATAcc                                                                                                    <  1:972661/139‑1 (MQ=255)
                       ggTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATtg                                                                                                                            <  1:1116948/113‑1 (MQ=255)
                       ggTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATtg                                                                                                                            >  2:1116948/1‑113 (MQ=255)
                       ggTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                               <  2:312465/126‑1 (MQ=255)
                       ggTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                               >  1:312465/1‑126 (MQ=255)
                        gTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                               >  2:158248/1‑125 (MQ=255)
                        gTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTaaa                                                                                                               <  1:158248/125‑1 (MQ=255)
                         tACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                                <  1:1006125/139‑1 (MQ=255)
                         tACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                                <  1:1162219/139‑1 (MQ=255)
                                ttGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                                >  2:852746/1‑132 (MQ=255)
                                ttGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                                <  1:852746/132‑1 (MQ=255)
                                  gACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATtata                                                                                                      >  1:1284024/1‑124 (MQ=255)
                                  gACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATtata                                                                                                      <  2:1284024/124‑1 (MQ=255)
                                     acCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAagaga                                                                                    <  2:982084/139‑1 (MQ=255)
                                              gACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCt                                                                           <  2:324601/139‑1 (MQ=255)
                                                   tGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTc                                                                      <  2:1267753/139‑1 (MQ=255)
                                                         gcgcGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGa                                                                <  2:543471/139‑1 (MQ=255)
                                                         gcgcGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGa                                                                >  2:1313451/1‑139 (MQ=255)
                                                          cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAAt                                                                                                                              >  2:888040/1‑76 (MQ=255)
                                                          cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAAt                                                                                                                              <  1:888040/76‑1 (MQ=255)
                                                          cgcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGaa                                                               >  2:271948/1‑139 (MQ=255)
                                                           gcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTc                                                                      >  1:485070/1‑131 (MQ=255)
                                                           gcgACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTc                                                                      <  2:485070/131‑1 (MQ=255)
                                                                 aaaaTGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATaaa                                                        <  2:744913/139‑1 (MQ=255)
                                                                             gggATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTa                                            <  1:271948/139‑1 (MQ=255)
                                                                                         aGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCg                                                                 <  2:772835/106‑1 (MQ=255)
                                                                                         aGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCg                                                                 >  1:772835/1‑106 (MQ=255)
                                                                                         aGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGaaaa                                >  2:767779/1‑139 (MQ=255)
                                                                                             tCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATta                                                                                                        <  1:330457/63‑1 (MQ=255)
                                                                                             tCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATta                                                                                                        >  2:330457/1‑63 (MQ=255)
                                                                                                gAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATAc                                                                                                     <  1:270213/63‑1 (MQ=255)
                                                                                                gAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATAc                                                                                                     >  2:270213/1‑63 (MQ=255)
                                                                                                gAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTccc                                                                              <  2:59521/86‑1 (MQ=255)
                                                                                                gAAAAACCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTccc                                                                              >  1:59521/1‑86 (MQ=255)
                                                                                                     aCCTCCTGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGa                    <  2:425053/139‑1 (MQ=255)
                                                                                                          ctGTTGTACCGTCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGATGCAg               <  1:1313451/139‑1 (MQ=255)
                                                                                                                     tCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCt                                                                           >  1:115943/1‑68 (MQ=255)
                                                                                                                     tCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCt                                                                           <  2:115943/68‑1 (MQ=255)
                                                                                                                     tCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAg                       >  2:218472/1‑120 (MQ=255)
                                                                                                                     tCCATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAg                       <  1:218472/120‑1 (MQ=255)
                                                                                                                       cATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                                >  2:938814/1‑45 (MQ=255)
                                                                                                                       cATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGAt                                                                                                <  1:938814/45‑1 (MQ=255)
                                                                                                                       cATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGATGCAGGaaaa          >  1:467897/1‑131 (MQ=255)
                                                                                                                       cATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGATGCAGGaaaa          <  2:467897/131‑1 (MQ=255)
                                                                                                                       cATAATCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGATGCAGGAAAATAGTCCtt  >  2:23969/1‑139 (MQ=255)
                                                                                                                          aaTCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGtttt                                                 <  2:983833/89‑1 (MQ=255)
                                                                                                                          aaTCAGTAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGtttt                                                 >  1:983833/1‑89 (MQ=255)
                                                                                                                                |                                                                                                                                 
CTACTGTCCACTGATAGCCCTGCGGTACGATTTTGACACCCGCGCCGACAATGACCAGCGCGACAAAAATGAGAATCGGGATAAAGATAAGCATCGGAAAAACCTCCTGTTGTACCGTCCATAATCAGCAAAATTGCTGCTTGATTAAACAAATTATACCTGATTACTGAAAGAGAGTTCCCCCTTATTCCTGCGAAGGATAAACTGTTTTTAGTAAAAATCAGAAAAAGGGAACAGCGATGCAGGAAAATAGTCCTT  >  NC_000913/515680‑515937

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