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
A3 F1 I1 R1 502 34.8 1912488 98.2% 1878063 80.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,559,491 G→A W408* (TGG→TGA)  rtcR → DNA‑binding transcriptional activator RtcR

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,559,4910GA100.0% 160.1 / NA 44W408* (TGG→TGA) rtcRDNA‑binding transcriptional activator RtcR
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (17/27);  total (17/27)

ACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGG  >  NC_000913/3559414‑3559567
                                                                             |                                                                            
actGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGacgc                                                                           <  2:676436/81‑1 (MQ=255)
actGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGacgc                                                                           <  2:676438/81‑1 (MQ=255)
    gCGACAGCGTGCGTTTTACCACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCTACCTCTCCCCAGGCAACATGACGCGGTa                                                                       <  1:676439/81‑1 (MQ=255)
       aCAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACt                                                                    >  2:676506/1‑81 (MQ=255)
         aGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACttt                                                                  >  2:676521/1‑81 (MQ=255)
          gcgtgcgtTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTc                                                                 <  1:676440/81‑1 (MQ=255)
          gcgtgcgtTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTc                                                                 <  2:676441/81‑1 (MQ=255)
           cgtgcgtTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTcg                                                                <  1:676442/81‑1 (MQ=255)
             tgcgtTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTcgcg                                                              <  2:676443/81‑1 (MQ=255)
                gtTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAAc                                                           <  1:676444/81‑1 (MQ=255)
                   ttAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACtt                                                         <  1:676445/80‑1 (MQ=255)
                    tAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACttt                                                        <  2:676446/80‑1 (MQ=255)
                    tAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACttt                                                        <  2:676447/80‑1 (MQ=255)
                     aaCACCGAAGCGCTGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCt                                                      >  1:676519/1‑81 (MQ=255)
                     aaCACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTc                                                       <  2:676448/80‑1 (MQ=255)
                      acacCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCt                                                      <  2:676449/80‑1 (MQ=255)
                        acCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGcc                                                   <  2:676451/81‑1 (MQ=255)
                        acCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGcc                                                   <  1:676450/81‑1 (MQ=255)
                          cGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAg                                                 <  1:676452/81‑1 (MQ=255)
                           gAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGc                                                >  1:676523/1‑81 (MQ=255)
                            aaGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCg                                               >  1:676503/1‑81 (MQ=255)
                            aaGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCg                                               <  1:676453/81‑1 (MQ=255)
                                gcggcgcgCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCAc                                           >  2:676528/1‑81 (MQ=255)
                                  ggcgcgCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCAcgc                                         >  1:676516/1‑81 (MQ=255)
                                    cgcgcCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCgg                                       <  1:676454/81‑1 (MQ=255)
                                    cgcgcCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCgg                                       <  1:676455/81‑1 (MQ=255)
                                      cgcCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGAt                                     <  2:676456/81‑1 (MQ=255)
                                       gcCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATg                                    >  1:676517/1‑81 (MQ=255)
                                           ggTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCa                                >  2:676525/1‑81 (MQ=255)
                                            gTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGcc                                 <  2:676458/79‑1 (MQ=255)
                                            gTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGcc                                 <  1:676459/79‑1 (MQ=255)
                                            gTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCa                                <  1:676457/80‑1 (MQ=255)
                                            gTTGGCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCAc                               <  2:676460/81‑1 (MQ=255)
                                                gCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCttt                           <  1:676462/81‑1 (MQ=255)
                                                gCTTTTGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCttt                           <  2:676461/81‑1 (MQ=255)
                                                   tttGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGc                         >  1:676508/1‑80 (MQ=255)
                                                   tttGCGACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGc                         >  2:676511/1‑80 (MQ=255)
                                                        gACCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAg                   >  1:676518/1‑81 (MQ=255)
                                                         aCCTCTCCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGc                  <  1:676463/81‑1 (MQ=255)
                                                            tctcCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGa               >  1:676513/1‑81 (MQ=255)
                                                             ctcCCCAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGAc              >  1:676504/1‑81 (MQ=255)
                                                               ccccAGGCAATATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACg             >  2:676520/1‑80 (MQ=255)
                                                               ccccAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACg             >  1:676515/1‑80 (MQ=255)
                                                                 ccAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCAt          >  1:676507/1‑81 (MQ=255)
                                                                  cAGGCAACATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATc         <  1:676464/81‑1 (MQ=255)
                                                                         cATGACGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTgg  <  1:676465/81‑1 (MQ=255)
                                                                             |                                                                            
ACTGGCGACAGCGTGCGTTTTAACACCGAAGCGCGGCGCGCCTGGTTGGCTTTTGCGACCTCTCCCCAGGCAACATGGCGCGGTAACTTTCGCGAACTTTCTGCCAGCGTCACGCGGATGGCCACCTTTGCCACTAGCGGACGCATCACTCTGG  >  NC_000913/3559414‑3559567

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A