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 F1 I2 R1 764 42.0 2018750 95.5% 1927906 109.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,803,567 G→A pseudogene (50/1476 nt) arpB → pseudogene, ankyrin repeats

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,803,5670GA100.0% 189.4 / NA 59pseudogene (50/1476 nt)arpBpseudogene, ankyrin repeats
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (31/28);  total (31/28)

TAACCATTTGCGAAGCATACTGGATTATATTGAACAGGAACAGTTAACTGCTGAAGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAGTGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAAT  >  NC_000913/1803432‑1803695
                                                                                                                                       |                                                                                                                                
tAACCATTTGCGAAGCATACTGGATTATATTGAACAGGAACAGTTAACTGCTGAAGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGc                                                                                                                               <  2:555611/139‑1 (MQ=255)
 aaCCATTTGCGAAGCATACTGGATTATATTGAACAGGAACAGTTAACTGCTGAAGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCa                                                                                                                              >  1:437769/1‑139 (MQ=255)
       ttGCGAAGCATACTGGATTATATTGAACAGGAACAGTTAACTGCTGAAGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGtttt                                                                                                                        >  2:598643/1‑139 (MQ=255)
            aaGCATACTGGATTATATTGAACAGGAACAGTTAACTGCTGAAGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCa                                                                                                                   <  1:886826/139‑1 (MQ=255)
                         tataTTGAACAGGAACAGTTAACTGCTGAAGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGAc                                                                                                      >  1:363161/1‑139 (MQ=255)
                           tatTGAACAGGAACAGTTAACTGCTGAAGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGc                                                                                                    <  2:363161/139‑1 (MQ=255)
                            atTGAACAGGAACAGTTAACTGCTGAAGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCt                                                                                                   >  1:1008148/1‑139 (MQ=255)
                                aacaggaacagTTAACTGCTGAAGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTAttt                                                                                               >  2:721989/1‑139 (MQ=255)
                                     gaacagTTAACTGCTGAAGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGt                                                                                          >  2:225751/1‑139 (MQ=255)
                                                   tgAAGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCAtt                                                                            >  2:587268/1‑139 (MQ=255)
                                                     aaGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGc                                                                          >  2:387291/1‑139 (MQ=255)
                                                         tCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATa                                                                      <  1:721989/139‑1 (MQ=255)
                                                            tAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGc                                                                   >  1:815941/1‑139 (MQ=255)
                                                                  ttGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCAt                                                                             <  1:548759/123‑1 (MQ=255)
                                                                  ttGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCAt                                                                             >  2:548759/1‑123 (MQ=255)
                                                                   tGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCAt                                                                             <  1:872439/122‑1 (MQ=255)
                                                                   tGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCAt                                                                             >  2:872439/1‑122 (MQ=255)
                                                                   tGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTAGCCATCTGTCATTGCAATACGCCCTTGAt                                                            >  2:923211/1‑139 (MQ=255)
                                                                       tGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCAt                                                        >  1:186797/1‑139 (MQ=255)
                                                                             tGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCa                                                                                                                   >  2:667669/1‑74 (MQ=255)
                                                                             tGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGaa                                                  <  1:333339/139‑1 (MQ=255)
                                                                             tGTCTAAAAAAATCAATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCa                                                                                                                   <  1:667669/74‑1 (MQ=255)
                                                                               tCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCa                                                                                     <  2:688728/102‑1 (MQ=255)
                                                                               tCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCa                                                                                     >  2:460100/1‑102 (MQ=255)
                                                                               tCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCa                                                                                     >  1:688728/1‑102 (MQ=255)
                                                                               tCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCa                                                                                     <  1:460100/102‑1 (MQ=255)
                                                                               tCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGt                                                                                >  2:926280/1‑107 (MQ=255)
                                                                               tCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGt                                                                                <  1:926280/107‑1 (MQ=255)
                                                                               tCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAAt                                                >  2:931924/1‑139 (MQ=255)
                                                                                 tAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTg                                                                                                                     >  2:69957/1‑68 (MQ=255)
                                                                                 tAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTg                                                                                                                     <  1:69957/68‑1 (MQ=255)
                                                                                         tCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTg                                                                                                        <  1:573892/73‑1 (MQ=255)
                                                                                         tCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTg                                                                                                        >  2:573892/1‑73 (MQ=255)
                                                                                         tCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCa                                      >  1:242100/1‑139 (MQ=255)
                                                                                           cATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCaaa                                    <  1:917879/139‑1 (MQ=255)
                                                                                                agaAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCaa                               <  2:687596/139‑1 (MQ=255)
                                                                                                 gaAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAAc                              <  2:242100/139‑1 (MQ=255)
                                                                                                 gaAAAAAACTATACACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAAc                              <  1:598643/139‑1 (MQ=255)
                                                                                                            taCACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAAt                                                                                                                 >  2:223603/1‑45 (MQ=255)
                                                                                                            taCACCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAAt                                                                                                                 <  1:223603/45‑1 (MQ=255)
                                                                                                              cacCCAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACAtt                 >  1:861785/1‑139 (MQ=255)
                                                                                                                 ccAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTAct              >  2:378748/1‑139 (MQ=255)
                                                                                                                  cAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAATGTCAACCTGATTAAACATTa                >  1:761954/1‑136 (MQ=255)
                                                                                                                  cAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAATGTCAACCTGATTAAACATTa                <  2:761954/136‑1 (MQ=255)
                                                                                                                  cAACAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTActc             <  1:931924/139‑1 (MQ=255)
                                                                                                                    aCAGTAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATAAGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTActcct           >  2:682754/1‑139 (MQ=255)
                                                                                                                        tAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGt       <  2:861785/139‑1 (MQ=255)
                                                                                                                        tAAATCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGt       <  1:225751/139‑1 (MQ=255)
                                                                                                                         aaaTCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGtt      <  2:899657/139‑1 (MQ=255)
                                                                                                                           aTCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGa                          >  1:740652/1‑117 (MQ=255)
                                                                                                                           aTCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGa                          <  2:740652/117‑1 (MQ=255)
                                                                                                                           aTCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGa    <  2:186797/139‑1 (MQ=255)
                                                                                                                           aTCTCAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGa    <  1:378748/139‑1 (MQ=255)
                                                                                                                             ctcAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAAt  >  1:84961/1‑139 (MQ=255)
                                                                                                                             ctcAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAAt  >  2:716804/1‑139 (MQ=255)
                                                                                                                               cAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGt       >  2:11694/1‑132 (MQ=255)
                                                                                                                               cAATGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGt       <  1:11694/132‑1 (MQ=255)
                                                                                                                                aaTGGTAATGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCAt                                                                             >  1:643196/1‑61 (MQ=255)
                                                                                                                                aaTGGTAATGCATCTTTTTTGCAAGCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCAt                                                                             <  2:643196/61‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                
TAACCATTTGCGAAGCATACTGGATTATATTGAACAGGAACAGTTAACTGCTGAAGATCGTAACCATTGTATGAAACTGTCTAAAAAAATCCATAGAGAAAAAAACTATACACCCAACAGTAAATCTCAATGGTAGTGCATGTTTTTTGCAATCTCCTTCTGACGCTATTTTTTGTCGCCATCTGTCATTGCAATACGCCCTTGATTCATTGAGAAATGGAAAAGGCAAAGTCAACCTGATTAAACATTACTCCTCCGTTGAAT  >  NC_000913/1803432‑1803695

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