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 F57 I1 R1 14 36.1 829726 89.5% 742604 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA CP000730 1,891,904 (T)6→5 coding (103/501 nt) rot ← repressor of toxins Rot

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,891,8990T.97.5% 177.4 / ‑1.7 40coding (108/501 nt)rotrepressor of toxins Rot
Reads supporting (aligned to +/- strand):  ref base T (1/0);  new base . (19/20);  total (20/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.01e-01

TTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTACTTTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAA  >  CP000730/1891762‑1892027
                                                                                                                                         |                                                                                                                                
ttttGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTACtttt                                                                                                                               >  2:156476/1‑141 (MQ=255)
    gCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATCCCAAATACAGTGTCGTTATTTACTTTTTTCa                                                                                                                           >  1:350218/1‑141 (MQ=255)
       aTAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCt                                                                                                                       >  1:98349/1‑141 (MQ=255)
       aTAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTNTCATGCt                                                                                                                       >  2:310426/1‑141 (MQ=255)
                     attaaaattTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAAt                                                                                                         >  2:373073/1‑141 (MQ=255)
                      ttaaaattTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCACATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAAtt                                                                                                        <  2:413501/141‑1 (MQ=255)
                         aaattTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATtaat                                                                                                     <  2:379354/141‑1 (MQ=255)
                         aaattTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATtaat                                                                                                     <  1:183166/141‑1 (MQ=255)
                         aaattTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATtaat                                                                                                     <  1:389068/141‑1 (MQ=255)
                              tcttctCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATca                                                                                                <  2:231872/141‑1 (MQ=255)
                              tcttctCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATca                                                                                                <  2:52514/141‑1 (MQ=255)
                               cttctCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATcac                                                                                               <  2:98385/141‑1 (MQ=255)
                                         cATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGct                                                                                     >  1:27183/1‑141 (MQ=255)
                                         cATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGct                                                                                     <  1:296539/141‑1 (MQ=255)
                                                 aTTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACa                                                                             <  2:218181/141‑1 (MQ=255)
                                                 aTTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACa                                                                             <  1:158513/141‑1 (MQ=255)
                                                 aTTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACa                                                                             <  2:375961/141‑1 (MQ=255)
                                                    cGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGt                                                                          >  2:126426/1‑141 (MQ=255)
                                                    cGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGt                                                                          >  2:155049/1‑141 (MQ=255)
                                                    cGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGt                                                                          >  1:7072/1‑141 (MQ=255)
                                                           aaTCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTaaca                                                                   >  1:291796/1‑141 (MQ=255)
                                                           aaTCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGATTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTaaca                                                                   >  1:218705/1‑141 (MQ=255)
                                                             tctcGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTaacaaa                                                                 >  2:356923/1‑141 (MQ=255)
                                                                cGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACAt                                                              >  2:215783/1‑141 (MQ=255)
                                                                cGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACAt                                                              >  2:28927/1‑141 (MQ=255)
                                                                cGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACAt                                                              >  2:8021/1‑141 (MQ=255)
                                                                cGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACAt                                                              >  1:117284/1‑141 (MQ=255)
                                                                cGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACAt                                                              >  1:22937/1‑141 (MQ=255)
                                                                 gCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATc                                                             >  2:378217/1‑141 (MQ=255)
                                                                              ttAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCaa                                                <  2:27183/141‑1 (MQ=255)
                                                                                  tGTCACCCAAACGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACt                                            <  2:159261/141‑1 (MQ=255)
                                                                                     cACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACCGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATCCAAGTATTAACAAACACCCCAACAATCCCAAAACTTGt                                         >  2:327597/1‑141 (MQ=255)
                                                                                     cACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCTCAAAACTTGt                                         >  2:307123/1‑141 (MQ=255)
                                                                                                  ttCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TGTTTCATGCTAAACATCTCCCAATTAATTATCACATATTTAGCTACTATACCAGTATTAACAAACATCCCAACAATCCCACAACTTGTATGTGCTAACTTa                            <  1:402965/141‑1 (MQ=255)
                                                                                                        ttGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATTCATa                      <  1:72212/141‑1 (MQ=255)
                                                                                                        ttGCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATa                      <  2:231073/141‑1 (MQ=255)
                                                                                                          gCAAAATTCCAAATACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATaaa                    >  2:155900/1‑141 (MQ=255)
                                                                                                                    aaaTACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAgtg          <  1:8021/141‑1 (MQ=255)
                                                                                                                    aaaTACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAgtg          <  1:28927/141‑1 (MQ=255)
                                                                                                                    aaaTACAGTGTCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAgtg          <  2:22937/141‑1 (MQ=255)
                                                                                                                            tgtCGTTATTTAC‑TTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGtaaataaa  <  1:373073/141‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                
TTTTGCCATAAAGTTAGTAAAATTAAAATTTCTTCTCTAGACATTTTGTATTCGCTTTCAATCTCGCTGAAAATTGAGTTAATGTCACCCAAAAGTGTTTCTAATTGCAAAATTCCAAATACAGTGTCGTTATTTACTTTTTTCATGCTAAACATCTCCCAATTAATAATCACATATTTAGCTACTATACAAGTATTAACAAACATCCCAACAATCCCAAAACTTGTATGTGCTAACTTATGCATAAAACTACAAGTGTAAATAAA  >  CP000730/1891762‑1892027

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A