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
A5 F28 I1 R2 164 48.3 4710601 85.3% 4018142 55.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 3,824,326 T→C pseudogene (459/687 nt) rph → ECK3633:JW3618:b3643; ribonuclease PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,824,3260TC100.0% 210.5 / NA 56pseudogene (459/687 nt)rphECK3633:JW3618:b3643; ribonuclease PH
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (33/23);  total (33/23)

CGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGT  >  W3110S.gb/3824269‑3824382
                                                         |                                                        
cGTGGCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCg                                                       >  1:54993/1‑61 (MQ=255)
   ggCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   <  1:2031304/62‑1 (MQ=255)
   ggCGCTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   <  1:1827597/62‑1 (MQ=255)
    gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   <  1:3464151/61‑1 (MQ=255)
    gcgcTGGCAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   <  1:1495501/61‑1 (MQ=255)
             gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt                                         <  1:3102161/62‑1 (MQ=255)
             gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt                                         <  1:2665577/62‑1 (MQ=255)
             gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt                                         <  1:1980121/62‑1 (MQ=255)
             gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt                                         <  1:4563933/62‑1 (MQ=255)
             gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt                                         <  1:448884/62‑1 (MQ=255)
             gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt                                         <  1:3506316/62‑1 (MQ=255)
             gATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt                                         <  1:3965107/62‑1 (MQ=255)
                 cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   >  1:78199/1‑48 (MQ=255)
                 cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   >  1:4277511/1‑48 (MQ=255)
                 cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   >  1:3530195/1‑48 (MQ=255)
                 cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   >  1:3592123/1‑48 (MQ=255)
                 cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   >  1:4704936/1‑48 (MQ=255)
                 cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   >  1:4103166/1‑48 (MQ=255)
                 cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   >  1:1266836/1‑48 (MQ=255)
                 cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   >  1:1449984/1‑48 (MQ=255)
                 cgcTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGa                                                   >  1:537519/1‑48 (MQ=255)
                      cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAg                                       <  1:2574759/55‑1 (MQ=255)
                      cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAg                                       <  1:753218/55‑1 (MQ=255)
                      cAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAg                                       <  1:1509406/55‑1 (MQ=255)
                      cAGAAGCTGGGGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAg                                       <  1:3183947/55‑1 (MQ=255)
                        gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt                              >  1:1793080/1‑62 (MQ=255)
                        gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt                              >  1:2884725/1‑62 (MQ=255)
                        gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt                              >  1:4607897/1‑62 (MQ=255)
                        gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt                              >  1:3464540/1‑62 (MQ=255)
                        gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt                              >  1:1381598/1‑62 (MQ=255)
                        gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt                              >  1:608828/1‑62 (MQ=255)
                        gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt                              >  1:1273636/1‑62 (MQ=255)
                        gAAGCTGGTGGAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGttt                              >  1:757508/1‑62 (MQ=255)
                             tggtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTc                         >  1:697198/1‑62 (MQ=255)
                             tggtggAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTc                         >  1:4385586/1‑62 (MQ=255)
                                  gAAAACGGCAAGCTGAAAACCAACCCGATGAAAGGGATGGt                                         <  1:242175/41‑1 (MQ=255)
                                           aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg            >  1:1252895/1‑61 (MQ=255)
                                           aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg            >  1:4428260/1‑61 (MQ=255)
                                           aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg            >  1:3919510/1‑61 (MQ=255)
                                           aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg            >  1:1254280/1‑61 (MQ=255)
                                           aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg            >  1:2764336/1‑61 (MQ=255)
                                           aaGCTGAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACg            >  1:2561043/1‑61 (MQ=255)
                                                gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa       >  1:4417425/1‑61 (MQ=255)
                                                gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa       >  1:3245740/1‑61 (MQ=255)
                                                gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa       >  1:3015540/1‑61 (MQ=255)
                                                gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa       >  1:4547675/1‑61 (MQ=255)
                                                gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa       >  1:2903051/1‑61 (MQ=255)
                                                gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa       >  1:2729571/1‑61 (MQ=255)
                                                gAAAACCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGaa       >  1:1502545/1‑61 (MQ=255)
                                                    aCCAACCCGATGACAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat  <  1:4634284/62‑4 (MQ=255)
                                                    aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat  <  1:1226047/62‑4 (MQ=255)
                                                    aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat  <  1:1308102/62‑4 (MQ=255)
                                                    aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat  <  1:2311555/62‑4 (MQ=255)
                                                    aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat  <  1:2494547/62‑4 (MQ=255)
                                                    aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat  <  1:3364905/62‑4 (MQ=255)
                                                    aCCAACCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGTATTGTAAACGGTGAAGcaat  <  1:3477025/62‑4 (MQ=255)
                                                         |                                                        
CGTGGCGCTGGTAGATGCGCTACAGAAGCTGGTGGAAAACGGCAAGCTGAAAACCAATCCGATGAAAGGGATGGTAGCCGCAGTTTCTGTCGGAATTGTGAACGGCGAAGCGGT  >  W3110S.gb/3824269‑3824382

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A