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
A4 F1 I1 R1 73 24.7 1166784 93.9% 1095610 107.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,594,132 (C)8→7 pseudogene (3856/3861 nt) yneO ← pseudogene, AidA homolog

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,594,1250C.100.0% 91.9 / NA 22pseudogene (1/1461 nt)yneOpseudogene, AidA homolog
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base . (11/11);  total (11/11)

GGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCC  >  NC_000913/1593996‑1594255
                                                                                                                                 |                                                                                                                                  
ggCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACAGTCCCCGGTTACCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGcccccccagg                                                                                                                           >  1:357140/1‑136 (MQ=255)
                        cGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAgt                                                                                                  >  2:358263/1‑139 (MQ=255)
                         gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGcccccc                                                                                                                               >  1:146934/1‑110 (MQ=255)
                         gTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGcccccc                                                                                                                               <  2:146934/110‑1 (MQ=255)
                              cGGTCAGTACATTCCCCCGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGag                                                                                            <  2:357140/139‑2 (MQ=255)
                                          tCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACAt                                                                                >  1:434682/1‑139 (MQ=255)
                                               ggTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGcccc                                                                                                                                 <  1:176481/86‑1 (MQ=255)
                                               ggTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGcccc                                                                                                                                 >  2:176481/1‑86 (MQ=255)
                                               ggTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac                                                                           >  1:215335/1‑139 (MQ=255)
                                                 tttCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                         <  2:215335/139‑1 (MQ=255)
                                                 tttCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGAATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                         <  1:358263/139‑1 (MQ=255)
                                                           tCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                         >  1:279925/1‑129 (MQ=255)
                                                           tCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCg                                                                         <  2:279925/129‑1 (MQ=255)
                                                                           ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt                                                                    <  2:275449/118‑1 (MQ=255)
                                                                           ccGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGtt                                                                    >  1:275449/1‑118 (MQ=255)
                                                                                ccgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATca                                                                              <  1:33247/103‑1 (MQ=255)
                                                                                ccgccATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATca                                                                              >  2:33247/1‑103 (MQ=255)
                                                                                                 gccgccGATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCg                         >  2:489674/1‑139 (MQ=255)
                                                                                                  ccgccgATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac                                                                           >  2:106340/1‑88 (MQ=255)
                                                                                                  ccgccgATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCacac                                                                           <  1:106340/88‑1 (MQ=255)
                                                                                                   cgccgATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCAt                                                                                                                       <  1:355905/43‑1 (MQ=255)
                                                                                                   cgccgATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCAt                                                                                                                       >  2:355905/1‑43 (MQ=255)
                                                                                                   cgccgATAGTGGTTTTAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGa                       >  1:116376/1‑139 (MQ=255)
                                                                                                               ttttAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCTCGACAGCGCACCGCTGTTATAGATATTAATGTGTTGACTTGTCATATTAATGGCAGATTCGGAACCGAAAGCAAt           <  1:123163/139‑1 (MQ=255)
                                                                                                                  tAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATAtt                                                           >  2:505260/1‑88 (MQ=255)
                                                                                                                  tAGCGACACGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATAtt                                                           <  1:505260/88‑1 (MQ=255)
                                                                                                                        cacGCAGTG‑CCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTccccccc  <  1:489674/139‑1 (MQ=255)
                                                                                                                                 |                                                                                                                                  
GGCCATTGTTTCCGGTATAGTTGCCGTTAACGGTCAGTACATTCCCCGGTTTCCCCCCTTCGCTATTCATTTGAACCGTGCCGCCATTCTCCAGGTTGCCGCCGATAGTGGTTTTAGCGACACGCAGTGCCCCCCCCAGGCATAACGTTCATATCACCTGCAGTGGTGACATTTCCCGACATCACACCGCTGTTATGGATATTAATGTGTTGACTTGCCATATTAATGGCAGAGTCGGAACCGAAAGCAATTTCCCCCCC  >  NC_000913/1593996‑1594255

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A