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
A5 F71 I1 R1 31 24.1 564604 94.3% 532421 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 2,018,810 (T)7→6 coding (109/810 nt) mgt ← Monofunctional glycosyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,018,8040T.100.0% 57.9 / NA 14coding (115/810 nt)mgtMonofunctional glycosyltransferase
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base . (7/7);  total (7/7)

AAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTGCTCCTTCTTT  >  USA300TCH1516_ALE/2018673‑2018935
                                                                                                                                   |                                                                                                                                   
aaaaCTACTTTTATTTTCAATTTTTCTTAGTTCATCCCCTTTAGCTCTTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACttttttcttt                                                                                                                            <  1:145609/141‑5 (MQ=255)
        ttttATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTcggcgg                                                                                                                   >  1:153914/1‑141 (MQ=255)
             ttttCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGc                                                                                                              <  1:267934/141‑1 (MQ=255)
             ttttCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATAACTGATTCCAATAAACAATGCGATAATGATGAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGc                                                                                                              <  2:86290/141‑1 (MQ=255)
                 cAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCTGCTGTTTGCCaat                                                                                                          >  2:89941/1‑140 (MQ=255)
                       ttCTTAGTTCATCCACATTATCGCGTGTAGATAACAAATACATGCTACCCATACACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTg                                                                                                    >  1:5350/1‑141 (MQ=255)
                           tAGTTCAACCACATTATCGAGTGTAGATAAAAAAGACATGATACCAATAAACTATGAGATATTTATTAGAATGGTTAATAAGATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGTCGGTTTGCCAACTGGTTGataa                                                                                                <  2:86386/141‑1 (MQ=255)
                                      caTTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATtata                                                                                     >  1:173537/1‑141 (MQ=255)
                                      caTTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGATTTGCCAACTGCTTGATAATACGTATtata                                                                                     >  1:51450/1‑141 (MQ=255)
                                                                     aCCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGt                                                      <  1:153814/141‑1 (MQ=255)
                                                                      ccAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGtt                                                     <  2:153914/141‑1 (MQ=255)
                                                                                  gCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCAtttgagtttg                                         >  1:8877/1‑141 (MQ=255)
                                                                                                           atatTTTTAATAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCg                >  1:25904/1‑141 (MQ=255)
                                                                                                                     tAGTATTCGTTTAC‑TTTTTTCTTTTTCGGCGGTCTGCCATCTCGTTTATTATATGTGTTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCCTTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTGCTCctt      <  2:200276/141‑1 (MQ=255)
                                                                                                                         aTTCGTTTAC‑TTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTGCTCCTTCttt  <  2:116999/141‑1 (MQ=255)
                                                                                                                                   |                                                                                                                                   
AAAACTACTTTTATTTTCAATTTTTCTTAGTTCATCCACATTATCGCGTGTAGATAAAAAATACATGATACCAATAAACAATGCGATAATGATTAGAATGGTTAATAATATTTTTAATAGTATTCGTTTACTTTTTTTCTTTTTCGGCGGTTTGCCAACTGGTTGATAATACGTATTATAGTGAGGTTCGTGTTTCATATGCTCAAAATGTTCATTTGAGTTTGAGTACCTATCGCTTCTTTTCATGCGTTTGCTCCTTCTTT  >  USA300TCH1516_ALE/2018673‑2018935

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A