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
A1 F28 I1 R1 354 41.7 3110465 93.1% 2895842 61.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 2,646,699 C→G Q1415H (CAG→CAC)  yfhM ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,646,6990CG100.0% 224.7 / NA 60Q1415H (CAG→CAC) yfhMconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base G (44/16);  total (44/16)

CGCGTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATT  >  W3110S.gb/2646654‑2646749
                                             |                                                  
cgcgTTACTTTCCTGCGTCGTTAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:539478/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACTCCTGGTGCGAAAGTGTGTTCAg                                   >  1:2065570/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTTCGAAAGTGTGTTCAg                                   >  1:1463022/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGaa                                              >  1:1988666/1‑52 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCa                                    >  1:2969523/1‑62 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:2828592/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:2275228/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:2299094/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:230766/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:234364/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:2371747/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:2435563/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:2583735/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:2668350/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:2711373/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:1178259/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:2941795/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:3018619/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:3039428/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:675334/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:708987/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:716414/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:757215/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:854736/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:1632608/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:1647991/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:2064017/1‑63 (MQ=255)
cgcgTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:1557577/1‑63 (MQ=255)
cgcgTTACTTTCCTGAGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAg                                   >  1:732389/1‑63 (MQ=255)
         ttCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTAc                         <  1:232205/64‑1 (MQ=255)
         ttCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTAc                         <  1:2066655/64‑1 (MQ=255)
          tCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTg                       >  1:1893423/1‑65 (MQ=255)
          tCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTg                       >  1:1664496/1‑65 (MQ=255)
          tCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTg                       >  1:2981617/1‑65 (MQ=255)
          tCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTg                       >  1:150653/1‑65 (MQ=255)
          tCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTg                       >  1:1106277/1‑65 (MQ=255)
          tCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTg                       >  1:950383/1‑65 (MQ=255)
             tGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTc                    >  1:2701440/1‑65 (MQ=255)
             tGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTc                    >  1:2666263/1‑65 (MQ=255)
             tGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTc                    >  1:1872330/1‑65 (MQ=255)
             tGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTc                    >  1:2005174/1‑65 (MQ=255)
             tGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTc                    >  1:2020331/1‑65 (MQ=255)
             tGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTc                    >  1:918695/1‑65 (MQ=255)
             tGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTc                    >  1:530186/1‑65 (MQ=255)
             tGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTc                    >  1:1567390/1‑65 (MQ=255)
             tGCGTCGATAGCCAGCGTTCACCAAACGCCTGGTGCGAAAGTGTGTTCAGAAAAGTGTACTGCTc                    >  1:1965907/1‑65 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:1798827/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:1539120/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:867556/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:695081/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:53086/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:398690/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:2232943/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:1832451/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:2760913/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:2645627/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:2583044/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:2175283/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTAtt  <  1:2220940/65‑1 (MQ=255)
                               tCACCAAACGCCTGGTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCAACGGGTAGCAGTTTAtt  <  1:2720034/65‑1 (MQ=255)
                                             |                                                  
CGCGTTACTTTCCTGCGTCGATAGCCAGCGTTCACCAAACGCCTGCTGCGAAAGTGTGTTCAGCAAAGTGTACTGCTCATCGGGTAGCAGTTTATT  >  W3110S.gb/2646654‑2646749

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A