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
A1 F169 I0 R1 75 34.0 794130 95.7% 759982 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 2,679,455 Δ1 bp 100% intergenic (+327/‑62) USA300HOU_RS13790 → / → ssaA2_4 hypothetical protein/Staphylococcal secretory antigen ssaA2

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE2,679,4550A.100.0% 144.0 / NA 32intergenic (+327/‑62)USA300HOU_RS13790/ssaA2_4hypothetical protein/Staphylococcal secretory antigen ssaA2
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base . (17/15);  total (17/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

GTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTA  >  USA300TCH1516_ALE/2679318‑2679587
                                                                                                                                           |                                                                                                                                    
gTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAATTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTaaaa                                                                                                                                   >  1:102182/1‑141 (MQ=255)
           tctattaattGTTAAATACATGAATTTCTACATTTTATGAAATAATCCATTTTTATTACGATTCAACACTTTATATGACATCTTCATTACAGTTACTTTTATTGTTGATTGGTTAAATTG‑‑TATTAT‑AAAAAAATTTGTTAt                                                                                                                       <  2:9720/138‑1 (MQ=255)
           aCAATTAACTATTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTAt                                                                                                                       <  2:9639/141‑1 (MQ=255)
            cAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATc                                                                                                                      <  1:375635/141‑1 (MQ=255)
                 aattGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑‑AAAAAATTTGTTATCATAAtt                                                                                                                >  1:192348/1‑141 (MQ=255)
                  attGTTAAATACATAAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAAtt                                                                                                                >  1:260111/1‑141 (MQ=255)
                     gTTAAATACATGAATTTCTACCTTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAAc                                                                                                             <  1:181257/141‑1 (MQ=255)
                       tAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGt                                                                                                           <  1:211832/141‑1 (MQ=255)
                          aTACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGa                                                                                                        >  1:314038/1‑141 (MQ=255)
                              aTGAATTTCTACATTTTGTTAAAAAAGCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATaa                                                                                                    <  2:394617/141‑1 (MQ=255)
                              aTGAATTTCTACATTTTATGAAAAAATCCATTTTTATTATAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATaa                                                                                                    >  2:121127/1‑141 (MQ=255)
                                      cTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGaaaaaa                                                                                            <  1:177752/141‑1 (MQ=255)
                                       tACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGaaaaaaa                                                                                           <  1:324434/141‑1 (MQ=255)
                                        aCATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAAt                                                                                          <  2:238083/141‑1 (MQ=255)
                                         cATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAAtt                                                                                         <  1:308038/141‑1 (MQ=255)
                                                  aaaaaaTCCATTTTTATTACAATTCAACACTTTATAAGAAAAATTTTTTAATATTTATTTTATTTTTGATTTCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGga                                                                                <  2:278579/141‑1 (MQ=255)
                                                              tttATTACACTTCCACACTTTATATGACACCTTCCTTACTGTTAC‑CTAAATG‑TCAACACTATCATTGCAATTTCT‑AACAAAATTTGTTCTCGTAATTAACTTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGa                                                                    <  2:380187/141‑1 (MQ=255)
                                                                 attaCAATTCAACACTTTATATGACCACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAata                                                                 <  2:394692/141‑1 (MQ=255)
                                                                 attaCAATTCAACACTTTATATGACAACTTCATTACCGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAata                                                                 <  2:394757/141‑1 (MQ=255)
                                                                        ttCAACACTGTATATGACAAGTTCATTACAGCTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATaaaaaa                                                          >  2:299359/1‑140 (MQ=255)
                                                                        tctaaCACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCCTAATTAACGTTGAATAAAGAAAAAAATTAAATTGGTGGATAAAAATGGAGTATAAAAAg                                                          >  2:299419/4‑141 (MQ=255)
                                                                             cacTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACt                                                     >  1:316698/1‑141 (MQ=255)
                                                                                   atatGAAAACTTCTGTACATGTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAAAAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCg                                               <  1:173371/141‑1 (MQ=255)
                                                                                               cATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGc                                   >  2:344607/1‑141 (MQ=255)
                                                                                               cATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGc                                   >  2:376373/1‑141 (MQ=255)
                                                                                                aTTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATAATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCt                                  >  1:92366/1‑141 (MQ=255)
                                                                                                   aCAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCtttt                               >  2:345535/1‑141 (MQ=255)
                                                                                                           ttttATTGTTGATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACt                       >  2:106295/1‑141 (MQ=255)
                                                                                                                ttgttgATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTtct                  >  2:318645/1‑141 (MQ=255)
                                                                                                                    tgATTGCTTACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTcagc              >  1:117003/1‑141 (MQ=255)
                                                                                                                           ttACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTATCGATGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTc       >  2:65023/1‑141 (MQ=255)
                                                                                                                           ttACATTG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTc       >  2:320268/1‑141 (MQ=255)
                                                                                                                                ttG‑‑TTTTCT‑AAAAAAATTTGTTATCATAATTAACGTTGGATACAGAAAATCCGTCACTGGGGAGATAAAAATGGAATATAAAAAGATACTGATCGGCTTGTGAGTGGCGTTGGCAGTACTATCCTCAGCAGAGGTCACTTa  >  1:132119/1‑141 (MQ=255)
                                                                                                                                           |                                                                                                                                    
GTATCACTATGACAATTAATTGTTAAATACATGAATTTCTACATTTTATGAAAAAATCCATTTTTATTACAATTCAACACTTTATATGACAACTTCATTACAGTTACTTTTATTGTTGATTGCTTACATTG‑‑TTTTCTAAAAAAAATTTGTTATCATAATTAACGTTGAATAAAGAAAAAAATTAACTTGGGAGATAAAAATGGAATATAAAAAGATACTAATTCGTTTATTAATTGCTTTTGCAGTACTTTTCTCAGCAGATTTCACTTA  >  USA300TCH1516_ALE/2679318‑2679587

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A