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 2,521,593 C→T *295* (TAG→TAA)  xapR ← transcriptional activator of xapAB

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,521,5930CT100.0% 195.1 / NA 60*295* (TAG→TAA) xapRtranscriptional activator of xapAB
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (30/30);  total (30/30)

ACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACCTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCAT  >  NC_000913/2521481‑2521718
                                                                                                                |                                                                                                                             
accaATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTgtgt                                                                                                                       <  2:1648655/121‑1 (MQ=255)
accaATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTgtgt                                                                                                                       >  1:1648655/1‑121 (MQ=255)
        aaaaaaGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                             <  1:1598711/139‑1 (MQ=255)
               cgcCCTAATGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCa                                                                                                            <  1:1083076/117‑1 (MQ=255)
               cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCa                                                                                                            >  2:1083076/1‑117 (MQ=255)
               cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGc                                                                                        <  2:763047/137‑1 (MQ=255)
               cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGc                                                                                        <  2:711189/137‑1 (MQ=255)
               cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGc                                                                                        >  1:763047/1‑137 (MQ=255)
               cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGc                                                                                        >  1:711189/1‑137 (MQ=255)
               cgcCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                      >  1:142706/1‑139 (MQ=255)
                  ccTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCAc                                                                                   <  2:647269/139‑1 (MQ=255)
                         gcgcTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCGCCTGCtgt                                                                            >  1:1016522/1‑139 (MQ=255)
                            cTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                      <  2:98334/126‑1 (MQ=255)
                            cTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGt                                                                                      >  1:98334/1‑126 (MQ=255)
                            cTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTc                                                                                     <  2:653472/127‑1 (MQ=255)
                            cTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTc                                                                                     >  1:653472/1‑127 (MQ=255)
                                       tCTGCGATTTGTGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCa                                                                                                            <  1:1296326/93‑1 (MQ=255)
                                       tCTGCGATTTGTGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCa                                                                                                            >  2:1296326/1‑93 (MQ=255)
                                         tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCa                                                                                                            >  2:1558290/1‑91 (MQ=255)
                                         tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCa                                                                                                            <  1:1558290/91‑1 (MQ=255)
                                         tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAatat                                                            >  2:1552988/1‑139 (MQ=255)
                                         tGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAatat                                                            >  1:467922/1‑139 (MQ=255)
                                            gATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAAtatata                                                         <  2:647179/139‑1 (MQ=255)
                                              tttGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCt                                                                                                      >  1:593436/1‑92 (MQ=255)
                                              tttGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCt                                                                                                      <  2:593436/92‑1 (MQ=255)
                                                                   cTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGcc                                                                                                             >  2:140187/1‑64 (MQ=255)
                                                                   cTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGcc                                                                                                             <  1:140187/64‑1 (MQ=255)
                                                                    ttCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGa                                 >  1:887828/1‑139 (MQ=255)
                                                                    ttCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGa                                 >  1:942950/1‑139 (MQ=255)
                                                                     tCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACctg                                                                                >  1:829124/1‑91 (MQ=255)
                                                                     tCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACctg                                                                                <  2:829124/91‑1 (MQ=255)
                                                                        cTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAata                                                             <  1:1413997/107‑1 (MQ=255)
                                                                        cTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAata                                                             >  2:1413997/1‑107 (MQ=255)
                                                                           aGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATaa                                                        <  2:156215/109‑1 (MQ=255)
                                                                           aGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATaa                                                        >  1:156215/1‑109 (MQ=255)
                                                                                actactATTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                             >  2:1632213/1‑67 (MQ=255)
                                                                                actactATTTCCGGCAATTCCTGTCTCCACACTTACTGTGTCAATGCAGCCAACAGCTTAACCATcg                                                                                             <  1:1632213/67‑1 (MQ=255)
                                                                                  tactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACctgct                                                                              <  1:1116127/80‑1 (MQ=255)
                                                                                  tactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACctgct                                                                              >  2:1116127/1‑80 (MQ=255)
                                                                                  tactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACctg                                                                                <  1:787144/78‑1 (MQ=255)
                                                                                  tactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACctg                                                                                >  2:787144/1‑78 (MQ=255)
                                                                                  tactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                            >  2:574588/1‑82 (MQ=255)
                                                                                  tactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCtgt                                                                            <  1:574588/82‑1 (MQ=255)
                                                                                  tactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                <  1:837044/94‑1 (MQ=255)
                                                                                  tactaTTTCCGGCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                >  2:837044/1‑94 (MQ=255)
                                                                                            ggCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCa                                                                                                            >  2:1260596/1‑40 (MQ=255)
                                                                                            ggCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCa                                                                                                            <  1:1260596/40‑1 (MQ=255)
                                                                                            ggCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                <  2:1136846/84‑1 (MQ=255)
                                                                                            ggCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACa                                                                >  1:1136846/1‑84 (MQ=255)
                                                                                            ggCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAggg                                              <  2:474674/102‑1 (MQ=255)
                                                                                            ggCAATTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAggg                                              >  1:474674/1‑102 (MQ=255)
                                                                                               aaTTCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGt      <  1:1552988/139‑1 (MQ=255)
                                                                                                 ttCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCAc                                                                                   >  1:771561/1‑60 (MQ=255)
                                                                                                 ttCCTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCAc                                                                                   <  2:771561/60‑1 (MQ=255)
                                                                                                   ccTGTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCAt  <  2:467922/139‑1 (MQ=255)
                                                                                                      gTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                  <  2:1299939/72‑1 (MQ=255)
                                                                                                      gTCTCCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                  >  1:1299939/1‑72 (MQ=255)
                                                                                                       tctcCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTg                                                   <  2:1578464/86‑1 (MQ=255)
                                                                                                       tctcCTCACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTg                                                   >  1:1578464/1‑86 (MQ=255)
                                                                                                             cACTTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATaaa                                                                  <  1:433595/65‑1 (MQ=255)
                                                                                                                |                                                                                                                             
ACCAATGTAAAAAAGCGCCCTAAAGGCGCTTTTTTGCTATCTGCGATTTGCGAAATTGCCTGATGCGCTTCACTTAGCAGACTACTATTTCCGGCAATTCCTGTCTCCTCACCTACTGTGTCAATGCAGCCAACAGCTTAACCATCGCGGGCGTCACCTGCTGTGTTTCATAAACAATATATAAATCTGCAGGGATGCGCTGTTTGAGCGGACGGAAAATGACACCTGGCCAGTTCAT  >  NC_000913/2521481‑2521718

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A