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
A12 F1 I2 R1 766 55.6 2631458 94.7% 2491990 109.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,784,529 C→T pseudogene (483/1374 nt) ypjC ← pseudogene

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,784,5290CT100.0% 136.2 / NA 45pseudogene (483/1374 nt)ypjCpseudogene
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (25/20);  total (25/20)

TTTGTTTTCATATGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTCTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCTGCTTGCTT  >  NC_000913/2784400‑2784664
                                                                                                                                 |                                                                                                                                       
tttGTTTTCATATGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCAttt                                                                                                                                >  2:306978/1‑139 (MQ=255)
                        ttCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGa                                                                                                        >  2:1174994/1‑139 (MQ=255)
                         tCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGAt                                                                                                       <  2:406839/139‑1 (MQ=255)
                             tACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGc                                                                                                   <  1:19636/139‑1 (MQ=255)
                                       tGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTa                                                                                         >  1:708941/1‑139 (MQ=255)
                                       tGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTa                                                                                         >  1:182541/1‑139 (MQ=255)
                                            gcgTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGa                                                                                    >  2:1113168/1‑139 (MQ=255)
                                                         aaCACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGtt                                                                       <  1:306978/139‑1 (MQ=255)
                                                           cacTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACCTTTTCTTATATTATCGAAAAGGTTTTATTCAtt                                                                                                                                 <  2:984266/79‑1 (MQ=255)
                                                           cacTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACCTTTTCTTATATTATCGAAAAGGTTTTATTCAtt                                                                                                                                 >  1:984266/1‑79 (MQ=255)
                                                            acTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                      <  2:744662/89‑1 (MQ=255)
                                                            acTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                                      >  1:744662/1‑89 (MQ=255)
                                                                cgcgTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCAt                                                                                                                                  >  2:76422/1‑73 (MQ=255)
                                                                cgcgTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCAt                                                                                                                                  <  1:76422/73‑1 (MQ=255)
                                                                  cgTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAg                                                                         <  2:581312/128‑1 (MQ=255)
                                                                  cgTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAg                                                                         >  1:581312/1‑128 (MQ=255)
                                                                        actTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCGTTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACAttt                                                        >  1:1081973/1‑139 (MQ=255)
                                                                            ggCTTAAGTAAACGAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCctt                                                                                                <  2:761182/95‑1 (MQ=255)
                                                                            ggCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCatt                                                                                                >  1:761182/1‑95 (MQ=255)
                                                                              cTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGATTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTAATCGATAATATTTTAGTTTCAGAAAACACATTTTCATTg                                                  >  1:1102639/1‑139 (MQ=255)
                                                                                 aaGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGttt                                               >  1:183232/1‑139 (MQ=255)
                                                                                   gTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTc                                             <  2:183232/139‑1 (MQ=255)
                                                                                   gTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTc                                             <  2:1273934/139‑1 (MQ=255)
                                                                                    tAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTcc                                            <  1:1113168/139‑1 (MQ=255)
                                                                                    tAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTcc                                            <  2:547988/139‑1 (MQ=255)
                                                                                       aCCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGc                                         >  2:667887/1‑139 (MQ=255)
                                                                                           aCATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTa                                     >  1:214476/1‑139 (MQ=255)
                                                                                            cATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAg                                    >  1:974253/1‑139 (MQ=255)
                                                                                            cATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGACATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAg                                    >  2:1026174/1‑139 (MQ=255)
                                                                                                   aTCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGtt                                                                       >  2:1218575/1‑97 (MQ=255)
                                                                                                   aTCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGtt                                                                       <  1:1218575/97‑1 (MQ=255)
                                                                                                     cACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATgag                           <  2:353629/139‑1 (MQ=255)
                                                                                                                  attatCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAg              >  2:726634/1‑139 (MQ=255)
                                                                                                                     atCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGAcc           >  2:932974/1‑139 (MQ=255)
                                                                                                                     atCGAAAAGGTTTTATTCATTTCTTTTAGCACATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGAcc           >  2:1016873/1‑139 (MQ=255)
                                                                                                                      tCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACAtttt                                                       >  1:532855/1‑94 (MQ=255)
                                                                                                                      tCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACAtttt                                                       <  2:532855/94‑1 (MQ=255)
                                                                                                                      tCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGttt                                 <  1:1107676/116‑1 (MQ=255)
                                                                                                                      tCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGttt                                 >  2:1107676/1‑116 (MQ=255)
                                                                                                                       cGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCtg         <  2:708941/139‑1 (MQ=255)
                                                                                                                        gAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCtgc        <  2:79255/139‑1 (MQ=255)
                                                                                                                         aaaaGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGACATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCtgct       <  1:1026174/139‑1 (MQ=255)
                                                                                                                           aaGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGAt                      >  2:338281/1‑122 (MQ=255)
                                                                                                                           aaGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGAt                      <  1:338281/122‑1 (MQ=255)
                                                                                                                              gTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCTgcttgctt  >  1:1198411/1‑139 (MQ=255)
                                                                                                                                 |                                                                                                                                       
TTTGTTTTCATATGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTCTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCAGACCTGCTTGCTT  >  NC_000913/2784400‑2784664

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