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 F178 I0 R1 41 49.4 1100758 95.6% 1052324 140.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 665,392 T→G 100% L79* (TTA→TGA)  paiA_1 → Spermidine/spermine N(1)‑acetyltransferase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE665,3920TG100.0% 132.0 / ‑6.5 42L79* (TTA→TGA) paiA_1Spermidine/spermine N(1)‑acetyltransferase
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base G (20/20);  total (20/22)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

AACAGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGATAATAAAAATGAAGAA  >  USA300TCH1516_ALE/665258‑665528
                                                                                                                                      |                                                                                                                                        
aacaGTTAATCACTTTTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATAtt                                                                                                                                     >  1:407421/1‑140 (MQ=255)
aacaGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCCTTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATAtt                                                                                                                                     >  2:527544/1‑140 (MQ=255)
 acaGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAAAGATAttt                                                                                                                                    >  1:253548/1‑140 (MQ=255)
                  aGAATCCTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTa                                                                                                                   <  1:278796/140‑1 (MQ=255)
                    aaGCTTCATATAATGAACATCATTTAAAGAAAAGACTTAATGTACGATTATTCTTTGTCGTTGAAGAAGGTAATGTTATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTaaa                                                                                                                 <  1:41884/140‑1 (MQ=255)
                      gCTTCATATAATGAACATTTTTTAAATAAAAGACTACTAGAACAACTATCCTTCGTCGTTGAAGAAGGTAATGACATCGTTAGCCTTGGTAACTCTATTTACGGTGAAGACTGATATTTATCAGCTATTTATGTTAAAcc                                                                                                               >  2:120031/1‑140 (MQ=255)
                        ttCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGGTATCTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAg                                                                                                             <  1:488073/140‑1 (MQ=255)
                                  gAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGCAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGATCATTATGTTAACCCAGAATCGAAACa                                                                                                   >  1:272578/1‑140 (MQ=255)
                                     catcatTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATAc                                                                                                <  2:468340/140‑1 (MQ=255)
                                       tcatTTAAAGGAAGGACTTTAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCCTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAg                                                                                              <  1:464092/140‑1 (MQ=255)
                                         atTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGt                                                                                            >  2:306225/1‑140 (MQ=255)
                                           ttAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGttc                                                                                          >  2:97922/1‑139 (MQ=255)
                                            tAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTAt                                                                                         >  1:448932/1‑140 (MQ=255)
                                             aaagaaaagaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATg                                                                                        <  1:504184/140‑1 (MQ=255)
                                                     gaCTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCa                                                                                >  2:212427/1‑140 (MQ=255)
                                                         tCAAGAACAATTATTCTTAGTCGTTGAGGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGt                                                                            >  1:521773/1‑140 (MQ=255)
                                                         tCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAAGCGCAACATACAGGTTATGGTACAGCATTGt                                                                            <  2:334740/140‑1 (MQ=255)
                                                              aaCAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAAt                                                                       >  2:290492/1‑140 (MQ=255)
                                                              aaCAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATCGTTAAAt                                                                       >  2:367435/1‑140 (MQ=255)
                                                                      ttCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGAtt                                                               >  2:337430/1‑140 (MQ=255)
                                                                              cGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGtt                                                       >  2:257265/1‑140 (MQ=255)
                                                                                 tgatgaAGGTAATGACACCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTg                                                    <  2:16461/140‑1 (MQ=255)
                                                                                 tGAAGATGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTg                                                    <  2:74687/140‑1 (MQ=255)
                                                                                 tGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTg                                                    >  2:422538/1‑140 (MQ=255)
                                                                                 tGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCACAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTg                                                    <  1:329504/140‑1 (MQ=255)
                                                                                   aagaaaGTAATTACATCACTGGCTTTGCTAACTTTATTTACGCTAAAAAATGATATTTATCAGGTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGaa                                                  <  1:256548/140‑1 (MQ=255)
                                                                                      aagGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGAt                                               >  2:141565/1‑140 (MQ=255)
                                                                                        ggTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATaa                                             >  1:68959/1‑140 (MQ=255)
                                                                                            aTGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAAttt                                         <  2:456530/140‑1 (MQ=255)
                                                                                                cATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAg                                     >  1:545420/1‑140 (MQ=255)
                                                                                                  tctctGGCTTTGCTACCTTTCTTTCCGGTGAAGAATGATATGCATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGgt                                   <  2:448497/136‑1 (MQ=255)
                                                                                                   cGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGgtg                                  >  1:484287/1‑140 (MQ=255)
                                                                                                     ttttcTTTTCTAATTTTATTTGAGGTGAAGAATGATATTTATCAGGTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGtt                                <  1:123429/136‑1 (MQ=255)
                                                                                                     ttGGCTTTGCTAACTTTATTTACGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGtt                                <  1:381835/140‑1 (MQ=255)
                                                                                                               tAACTTTATTTACGGTGAAGAATGATATTTACCCGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAg                      <  2:431439/140‑1 (MQ=255)
                                                                                                                   tttatttaCGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGa                  <  2:448225/140‑1 (MQ=255)
                                                                                                                   tttatttaCGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGa                  <  1:527544/140‑1 (MQ=255)
                                                                                                                      cttgaCGGTAAATAATGATATTGATCAGCTCATTATGTTAAACAAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAACATGTAGTTGTTTACTTAGAAGTAGataa               <  2:253548/136‑1 (MQ=255)
                                                                                                                      atttaCGGTGAAGAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGataa               >  2:151620/1‑140 (MQ=255)
                                                                                                                       tttaCGGTGAAGAATTATATTTATCAGCTTATTATGTTAAACCATAATTGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGataat              <  1:215691/140‑1 (MQ=255)
                                                                                                                        ttaCGGTGTAAAATGATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGatattc             <  2:229898/140‑4 (MQ=255)
                                                                                                                                   aaTCATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGGGTTTACTTAGAAGTAGATAATAAAAATgaagaa  <  2:484743/140‑1 (MQ=255)
                                                                                                                                      |                                                                                                                                        
AACAGTTAATCACTTGTTAGAAGCTTCATATAATGAACATCATTTAAAGAAAAGACTTCAAGAACAATTATTCTTAGTCGTTGAAGAAGGTAATGACATCGTTGGCTTTGCTAACTTTATTTACGGTGAAGAATTATATTTATCAGCTCATTATGTTAAACCAGAATCGCAACATACAGGTTATGGTACAGCATTGTTAAATGAAGGATTATCACGTTTTGAAGATAAATTTGAAGGTGTTTACTTAGAAGTAGATAATAAAAATGAAGAA  >  USA300TCH1516_ALE/665258‑665528

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