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
A8 F1 I2 R1 765 53.2 2691310 93.4% 2513683 103.8

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% 101.8 / NA 33pseudogene (483/1374 nt)ypjCpseudogene
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (15/18);  total (15/18)

ATCTATTTTGTTTTCATATGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTCTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCA  >  NC_000913/2784394‑2784651
                                                                                                                                       |                                                                                                                          
aTCTATTTTGTTTTCATATGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTAt                                                                                                                         >  1:1022056/1‑139 (MQ=255)
    aTTTTGTTTTCATATGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCAt                                                                                                                     <  2:1022056/139‑1 (MQ=255)
    aTTTTGTTTTCATATGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCAt                                                                                                                     <  1:1293576/139‑1 (MQ=255)
                tatGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                         <  1:262873/139‑1 (MQ=255)
                  tGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCAt                                                                                                       <  1:19381/139‑1 (MQ=255)
                     aTTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCa                                                                                                    <  2:1050968/139‑1 (MQ=255)
                        aCGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCAt                                                                                                       >  1:42857/1‑133 (MQ=255)
                        aCGTCATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAATATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCAt                                                                                                       <  2:42857/133‑1 (MQ=255)
                              ttCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTATTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCGAAAAACTGa                                                                                           >  2:795078/1‑139 (MQ=255)
                                  aTACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCgg                                                                                       <  1:795078/139‑1 (MQ=255)
                                                                  acTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGCTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCa                                                       >  1:337328/1‑139 (MQ=255)
                                                                      cgcgTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGaaa                                                   >  1:16984/1‑139 (MQ=255)
                                                                           actactTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTa                                                                                                                          >  1:548735/1‑63 (MQ=255)
                                                                              actTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTAt                                                                                                                         <  2:4958/61‑1 (MQ=255)
                                                                              actTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTAt                                                                                                                         >  1:4958/1‑61 (MQ=255)
                                                                                 tGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCAtt                                                                                                      >  1:1193192/1‑77 (MQ=255)
                                                                                 tGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCAtt                                                                                                      <  2:1193192/77‑1 (MQ=255)
                                                                                       aaGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                         <  1:515955/68‑1 (MQ=255)
                                                                                       aaGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAgcgc                                                                                                         >  2:515955/1‑68 (MQ=255)
                                                                                         gTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTc                                <  2:16984/139‑1 (MQ=255)
                                                                                          tAAAGCTACATGTAAATCATTTTTTTTTATATTCTCTAAAAAGTTTTATTCATTTTTTTTAGCGCATTCAAAAATCTGTTCGGCATGCTTTTTATTCGATAAATTTTTAGTTTCAGAAAACACATTTTCATTGTTTTcc                               <  2:282039/139‑1 (MQ=255)
                                                                                              ccAACATGAAAATCACCTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCt                           <  2:415301/139‑1 (MQ=255)
                                                                                                  cATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCa                                                                                     >  2:1253748/1‑77 (MQ=255)
                                                                                                  cATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCa                                                                                     <  1:1253748/77‑1 (MQ=255)
                                                                                                   aTGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATc                                                                                         <  1:526708/72‑1 (MQ=255)
                                                                                                   aTGAAAATCACTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATc                                                                                         >  2:526708/1‑72 (MQ=255)
                                                                                                    tGAAAATCGCTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTGCAGCTTTCGtt                     >  1:874146/1‑139 (MQ=255)
                                                                                                            aCTTTTTCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATgaga             >  1:257861/1‑139 (MQ=255)
                                                                                                                tttCTTATATTATCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGAt         <  1:1232394/139‑1 (MQ=255)
                                                                                                                            tCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGAt         >  1:79901/1‑127 (MQ=255)
                                                                                                                            tCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGAt         <  2:79901/127‑1 (MQ=255)
                                                                                                                            tCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCa  >  1:725428/1‑134 (MQ=255)
                                                                                                                            tCGAAAAGGTTTTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCa  <  2:725428/134‑1 (MQ=255)
                                                                                                                                       |                                                                                                                          
ATCTATTTTGTTTTCATATGAATTACGTGATTCCATACAGACATTTGGCGGCGTTTCTAAAATAACACTACGCGTACTACTTGGCTTAAGTAAACCAACATGAAAATCACTTTTTCTTATATTATCGAAAAGGTTCTATTCATTTCTTTTAGCGCATTCAAAAAACTGATCGGCATTATTTTTATTCGATAATTTTTTAGTTTCAGAAAACACATTTTCATTGTTTTCCAGCTTTAGTTTAATGAGAAGATTTTCCCA  >  NC_000913/2784394‑2784651

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ 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