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
A19 F106 I0 R1 88 30.3 670850 93.2% 625232 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 2,337,959 C→T 100% intergenic (‑125/‑119) USA300HOU_2195 ← / → USA300HOU_2196 possible MerR family transcriptional regulator/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007302,337,9590CT100.0% 106.3 / NA 35intergenic (‑125/‑119)USA300HOU_2195/USA300HOU_2196possible MerR family transcriptional regulator/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (20/15);  total (20/15)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTG  >  CP000730/2337841‑2338095
                                                                                                                      |                                                                                                                                         
tATCCTTTCAGTTATCTTTGGTCGTCTAAAGTAATGTAGCTTTCTATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAACTTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATAACtt                                                                                                                     <  1:234869/141‑1 (MQ=255)
        cAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAAtt                                                                                                             <  2:121649/141‑1 (MQ=255)
                  tGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTa                                                                                                   >  2:161950/1‑141 (MQ=255)
                    gtcgtcTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTaaa                                                                                                 >  1:157361/1‑141 (MQ=255)
                          tAAAGTAATGTTGCTTCATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATAGTTTTTAATTACTTTTAAAATTGTATAACTTCAATAtttt                                                                                           >  2:233281/1‑140 (MQ=255)
                                gattttGCTTTATATGTTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTGAATTTGTCTCTTTTTTAACATTTTATATTTCCTCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATTTTTAAAATgt                                                                                     >  2:73101/5‑140 (MQ=255)
                                aaTGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTCCACCAATTTAAATTTGTCTCTTTTGTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑a                                                                                    >  1:159293/1‑141 (MQ=255)
                                    ttGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑Atata                                                                                >  1:120244/1‑141 (MQ=255)
                                     tGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATaa                                                                               <  2:103782/141‑1 (MQ=255)
                                     tGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATaa                                                                               >  2:263200/1‑141 (MQ=255)
                                       ttttATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATc                                                                             <  2:279892/140‑1 (MQ=255)
                                        tttATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCa                                                                            >  2:233515/1‑141 (MQ=255)
                                          tatataTTGTCATCTTCGTTTGTATGCTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATAGTTTTTATTTACTTTAAAAATTGTATAAATTAAATATTTAAAATG‑CTCTAATCACt                                                                          >  2:169656/1‑141 (MQ=255)
                                          tataccttGTCCTCTTCGTCTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACt                                                                          <  1:322126/135‑1 (MQ=255)
                                             atatTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTaaa                                                                       >  2:230885/1‑140 (MQ=255)
                                              tatTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGa                                                                      <  2:159239/141‑1 (MQ=255)
                                               atTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGAt                                                                     >  1:281914/1‑141 (MQ=255)
                                                 tGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGAttt                                                                   >  2:326453/1‑140 (MQ=255)
                                                   tCATCTTCGTTTGAATACTTCTTATTTTATTTCTCAAATGTAGTTTCGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGat                                                                 <  1:257392/141‑1 (MQ=255)
                                                           gTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATATTATTTa                                                         >  1:30812/1‑141 (MQ=255)
                                                           gTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATCTTTa                                                         >  2:297092/1‑141 (MQ=255)
                                                           gTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATAACTAAGATTGATAATATTTa                                                         >  1:30827/1‑141 (MQ=255)
                                                           gTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATGGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTa                                                         >  1:109075/1‑141 (MQ=255)
                                                               gAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTAAttt                                                     >  1:281659/1‑141 (MQ=255)
                                                                 aTACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTAAttttt                                                   >  2:50866/1‑141 (MQ=255)
                                                                                                  gTCTCTTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGAt                  >  1:265573/1‑141 (MQ=255)
                                                                                                     tctTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCg               >  1:270412/1‑141 (MQ=255)
                                                                                                      ctTTTTTAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCgg              <  1:233515/141‑1 (MQ=255)
                                                                                                           ttAACCTTTTATATTTCATCGTTTTTAATTAACTAAAAACTTGTTACACTTTAATATTTAAAATC‑ACCCCACTTCTAATATTGCCACTGGTTTAGTGGTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAAt         <  1:78378/141‑1 (MQ=255)
                                                                                                           ttAACATTTTATATTTCCTCGTTTTTAATTACTTCAATAATTATATAACTTAAATTTTTAAAATGCATA‑GATAACTAATATTGATAAGAATGAAGTTTTTTAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAAt         <  1:78365/141‑1 (MQ=255)
                                                                                                           ttAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAAt         <  1:330822/141‑1 (MQ=255)
                                                                                                            tAACATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAAtt        <  1:198558/141‑1 (MQ=255)
                                                                                                             aaCATGTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGCGGTACTGAAAAttt       <  2:73211/141‑1 (MQ=255)
                                                                                                               cATTTTATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTgg     <  2:288303/141‑1 (MQ=255)
                                                                                                                  tttATATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTATTTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTg  <  2:76934/141‑1 (MQ=255)
                                                                                                                      |                                                                                                                                         
TATCCTTTCAGTTATGTTTGGTCGTCTAAAGTAATGTTGCTTTATATATTGTCATCTTCGTTTGAATACTTCTTATTTTATTACTCAAATTTAAATTTGTCTCTTTTTTAACATTTTACATTTCATCGTTTTTAATTACTTTAAAAATTGTATAACTTAAATATTTAAAATG‑ATATAATCACTAAGATTGATAATATTTAATTTTTTGAAAATTATTTTAGTTGCAATTTTTGGGTGATGCGGAAAATTTGGGTG  >  CP000730/2337841‑2338095

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