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
A6 F1 I2 R1 67 27.9 1239648 95.3% 1181384 112.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,567,574 T→C T316A (ACC→GCC)  mdtM ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,567,5740TC100.0% 77.3 / NA 21T316A (ACC→GCC) mdtMmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (11/10);  total (11/10)

AGCGATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGTGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCACGCCAGATAAACCGCGGTTCGGTCGGATCTTTAACAAAACGCG  >  NC_000913/4567474‑4567705
                                                                                                    |                                                                                                                                   
aGCGATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTTGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGAcagca                                                                                               >  1:371233/1‑139 (MQ=255)
       cGGAGACGGTCCCTTTCGGTAACTTATCGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCATCACCGACCAAAGCCAGACGTTCGGCGACAGCAGATTGcc                                                                                        >  2:479048/1‑139 (MQ=255)
               gTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCa                                                                                >  1:187773/1‑139 (MQ=255)
                tCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGAcc                                                                                                                       <  1:330839/99‑1 (MQ=255)
                tCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGAcc                                                                                                                       >  2:330839/1‑99 (MQ=255)
                tCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCaa                                                                               >  1:128553/1‑139 (MQ=255)
                 cccTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAAc                                                                              >  2:419721/1‑139 (MQ=255)
                       cGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCgag                                                                        <  2:187773/139‑1 (MQ=255)
                               tATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGAc                                                                <  2:128553/139‑1 (MQ=255)
                                  tGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGt                                                                                                           >  1:472708/1‑93 (MQ=255)
                                  tGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGt                                                                                                           <  2:472708/93‑1 (MQ=255)
                                            cGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGAcc                                                                                                                       <  1:190505/71‑1 (MQ=255)
                                            cGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGAcc                                                                                                                       >  2:190505/1‑71 (MQ=255)
                                                   cGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCAc                                            <  1:508947/139‑1 (MQ=255)
                                                                ggAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGAt                                                                                            >  2:589345/1‑78 (MQ=255)
                                                                ggAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGAt                                                                                            <  1:589345/78‑1 (MQ=255)
                                                                ggAAAATCAAACCAATCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCACGCCAGATAAACcg                               >  2:153988/1‑139 (MQ=255)
                                                                ggAAAATCAAACCAATCCCGAAAGCAAACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGAc                                                                <  2:149227/106‑1 (MQ=255)
                                                                ggAAAATCAAACCAATCCCGAAAGCAAACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGAc                                                                >  1:149227/1‑106 (MQ=255)
                                                                              aTCCCGAAAGCATACAGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCACGCCAGATAAACCGCGGTTCGGTCGGAt                 <  2:270921/139‑1 (MQ=255)
                                                                                             aGACTGGCGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCACGCCAGATAAACCGCGGTTCGGTCGGATCTTTAACAAAAcgcg  <  1:419721/139‑1 (MQ=255)
                                                                                                    |                                                                                                                                   
AGCGATGCGGAGACGGTCCCTTTCGGTAACTTATTGGAAAACAGCGTAAAGCGGAATAAGGTCGGGAAAATCAAACCAATCCCGAAAGCATACAGACTGGTGCCCAGCACCGACCACAGCCAGACGTGCGGCGACAGCAGATTGCCGACAATCAACAGCGAGAGGCCGACCAGTTGAATGGGTACGGCACGCCAGATAAACCGCGGTTCGGTCGGATCTTTAACAAAACGCG  >  NC_000913/4567474‑4567705

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