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
A3 F1 I2 R1 58 36.1 1832140 90.7% 1661750 105.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 584,639 C→T intergenic (+209/+41) appY → / ← ompT global transcriptional activator, DLP12 prophage/DLP12 prophage, outer membrane protease VII, outer membrane protein 3b

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913584,6390CT100.0% 167.0 / NA 48intergenic (+209/+41)appY/ompTglobal transcriptional activator, DLP12 prophage/DLP12 prophage, outer membrane protease VII, outer membrane protein 3b
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (24/24);  total (24/24)

AACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCCCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATACCTGCTCCATTTTTGCTGTAGTCTGAAG  >  NC_000913/584503‑584759
                                                                                                                                        |                                                                                                                        
aaCCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCg                                                                                                                        >  2:338379/1‑139 (MQ=255)
                   ggTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCggg                                                                                                     <  2:553264/139‑1 (MQ=255)
                    gTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCgggg                                                                                                    <  2:752331/139‑1 (MQ=255)
                       gCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGaaa                                                                                                 >  2:536684/1‑139 (MQ=255)
                                            acTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTaaaa                                                                            >  1:406582/1‑139 (MQ=255)
                                            acTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTaaaa                                                                            >  2:406579/1‑139 (MQ=255)
                                                taATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGTGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAAtgtg                                                                        <  1:74099/139‑1 (MQ=255)
                                                 aaTTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATgtgt                                                                       >  1:486215/1‑139 (MQ=255)
                                                     gATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACtt                                                                   <  1:406579/139‑1 (MQ=255)
                                                      aTGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCggg                                                                                                     <  2:688489/104‑1 (MQ=255)
                                                      aTGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCggg                                                                                                     >  1:688489/1‑104 (MQ=255)
                                                      aTGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAAt                                                                           >  2:65946/1‑130 (MQ=255)
                                                      aTGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAAt                                                                           <  1:65946/130‑1 (MQ=255)
                                                      aTGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTa                                                                  >  1:587503/1‑139 (MQ=255)
                                                      aTGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTa                                                                  >  1:490775/1‑139 (MQ=255)
                                                            ttCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACca                                                            >  1:412332/1‑139 (MQ=255)
                                                                    gATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTgg                                                                                       <  2:889558/104‑1 (MQ=255)
                                                                    gATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTgg                                                                                       >  1:889558/1‑104 (MQ=255)
                                                                                aaCCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTtata                                        <  2:412332/139‑1 (MQ=255)
                                                                                 aCCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAg                                       <  2:406582/139‑1 (MQ=255)
                                                                                   cTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGtt                                     <  1:638408/139‑1 (MQ=255)
                                                                                    ttCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTaaa                                                                             <  2:442062/98‑1 (MQ=255)
                                                                                    ttCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTaaa                                                                             >  1:442062/1‑98 (MQ=255)
                                                                                     tCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCg                                                                                     >  1:896942/1‑89 (MQ=255)
                                                                                     tCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCg                                                                                     <  2:896942/89‑1 (MQ=255)
                                                                                     tCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGtttt                                   >  2:826560/1‑139 (MQ=255)
                                                                                     tCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGtttt                                   >  1:668741/1‑139 (MQ=255)
                                                                                     tCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATGTTAGTTGGCg                                                                                     >  1:558317/1‑89 (MQ=255)
                                                                                     tCTGGGTTTATTGTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTCGTTGGCg                                                                                     <  2:558317/89‑1 (MQ=255)
                                                                                      cTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTAc                                                                     <  1:490105/104‑1 (MQ=255)
                                                                                      cTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTAc                                                                     >  2:490105/1‑104 (MQ=255)
                                                                                       tGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCg                                                                                     <  2:359888/87‑1 (MQ=255)
                                                                                       tGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCg                                                                                     >  1:359888/1‑87 (MQ=255)
                                                                                            ttATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATAcc                            <  1:338379/139‑1 (MQ=255)
                                                                                                         tAATTGTTACATTGAAATGGCTAGTTATTCCTCgggg                                                                                                                     <  2:640589/37‑1 (MQ=255)
                                                                                                         tAATTGTTACATTGAAATGGCTAGTTATTCCTCgggg                                                                                                                     >  1:640589/1‑37 (MQ=255)
                                                                                                         tAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCgg                                                                                                      >  1:739953/1‑52 (MQ=255)
                                                                                                         tAATTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCgg                                                                                                      <  2:739953/52‑1 (MQ=255)
                                                                                                          aaTTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCg                                                                                     >  2:569922/1‑68 (MQ=255)
                                                                                                          aaTTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCg                                                                                     <  1:569922/68‑1 (MQ=255)
                                                                                                           aTTGTTACATTGAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATACCTGCTCCATTTTTGCt             <  2:78295/139‑1 (MQ=255)
                                                                                                                      gAAATGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATACCTGCTCCATTTTTGCTGTAGTCTGAAg  <  1:826560/139‑1 (MQ=255)
                                                                                                                       aaaTGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTgg                                                                                       >  2:8517/1‑53 (MQ=255)
                                                                                                                       aaaTGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTgg                                                                                       <  1:8517/53‑1 (MQ=255)
                                                                                                                         aTGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAg                                       >  1:796607/1‑99 (MQ=255)
                                                                                                                         aTGGCTAGTTATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAg                                       <  2:796607/99‑1 (MQ=255)
                                                                                                                                 ttATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATACCTGCTCCATTTTTGCTGTAGTCTg     <  1:71653/125‑1 (MQ=255)
                                                                                                                                 ttATTCCTCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATACCTGCTCCATTTTTGCTGTAGTCTg     >  2:71653/1‑125 (MQ=255)
                                                                                                                                        |                                                                                                                        
AACCATTAATTTGTAATTGGGTTGCTGTCGCCTATTTTATACATACTATAATTGATGGTTTTCTATGTGATTTAGTTAATAACCTTCTGGGTTTATTTTAAGGGTTAATTGTTACATTGAAATGGCTAGTTATTCCCCGGGGCGATTTTCACCTCGGGGAAATTTTAGTTGGCGTTCTTAAAATGTGTACTTAAGACCAGCAGTAGTGATGAAGTTATAGTTTTCTATACCTGCTCCATTTTTGCTGTAGTCTGAAG  >  NC_000913/584503‑584759

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A