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
A13 F1 I1 R1 86 24.1 1002126 98.1% 983085 121.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,228,728 C→T pseudogene (31/150 nt) mdtQ ← pseudogene, putative channel/filament proteins

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,228,7280CT100.0% 63.9 / NA 20pseudogene (31/150 nt)mdtQpseudogene, putative channel/filament proteins
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (9/11);  total (9/11)

GCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGCGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTGGCAATACATCAGTGGCAATAAAACGAC  >  NC_000913/2228592‑2228857
                                                                                                                                        |                                                                                                                                 
gCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGa                                                                                                                                 >  2:230935/1‑139 (MQ=255)
    tCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGc                                                                                                                             <  2:316051/139‑1 (MQ=255)
            aCCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATaaa                                                                                                                     <  1:482875/139‑1 (MQ=255)
                     aGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCAc                                                                                                            <  1:374930/139‑1 (MQ=255)
                       cgcCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGCTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGa                                                                                                          >  1:326914/1‑139 (MQ=255)
                           gTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCa                                                                                                      <  1:168320/139‑1 (MQ=255)
                            tGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCAt                                                                                                     >  1:391017/1‑139 (MQ=255)
                                         gtCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCa                                                                                        >  2:251554/1‑139 (MQ=255)
                                          tCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAg                                                                                       <  1:92798/139‑1 (MQ=255)
                                                  tgCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGaaa                                                                               >  2:251015/1‑139 (MQ=255)
                                                                              tGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCg                                                   >  2:77669/1‑139 (MQ=255)
                                                                                                   gcACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGt                              <  2:391017/139‑1 (MQ=255)
                                                                                                     acacCCGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTgg                            <  1:77669/139‑1 (MQ=255)
                                                                                                         ccGGCCAGCATCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTcg                                 <  2:438435/130‑1 (MQ=255)
                                                                                                         ccGGCCAGCATAAGTAACAGCGGAAAACAGGTAATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTcg                                 >  1:438435/1‑130 (MQ=255)
                                                                                                                  aTCAGTAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTGGCAATACATCAGTg               <  2:141072/139‑1 (MQ=255)
                                                                                                                       tAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTgg                            <  2:159569/121‑1 (MQ=255)
                                                                                                                       tAACAGCGGAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTgg                            >  1:159569/1‑121 (MQ=255)
                                                                                                                              ggAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTGGCAATACATCAGTGGCAATAAAACGa   >  2:193551/1‑139 (MQ=255)
                                                                                                                               gAAAACAGGTGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTGGCAATACATCAGTGGCAATAAAACGAc  <  1:251554/139‑1 (MQ=255)
                                                                                                                                        |                                                                                                                                 
GCTGTCTGGCCAACCATTTTCAGCGCCGTGGGTAATGCGGTGTCAACTTGTGCAGCGGGCGTTTGCTGGCTTAACGCCTGGCGGGTTTCATGCATAGGCGCACACCCGGCCAGCATCAGTAACAGCGGAAAACAGGCGATGGCTGGATAAAAGGAATCACGATTCATGGGGGAATAATCAGGTAAGAAAAGGTGCGCGGAGATTACCGTGTGTTGCGATATATTTTTTAGTTTCGCGTGGCAATACATCAGTGGCAATAAAACGAC  >  NC_000913/2228592‑2228857

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A