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 F1 I2 R1 765 46.1 2269152 93.8% 2128464 105.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,330,357 +T coding (1395/1434 nt) dacB → D‑alanyl‑D‑alanine carboxypeptidase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,330,3531.T97.2% 112.0 / ‑3.9 36coding (1391/1434 nt)dacBD‑alanyl‑D‑alanine carboxypeptidase
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base T (18/17);  total (18/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTGCAGGGGGTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCG‑T‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAGTCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTT  >  NC_000913/3330223‑3330456
                                                                                                                                   |                                                                                                        
ttGCAGGGGGTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCG‑t‑ttttgaa                                                                                                 <  1:888057/139‑5 (MQ=255)
 tGCAGGGGGTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCG‑t‑ttttgaaa                                                                                                <  2:866567/139‑6 (MQ=255)
      ggggTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            <  1:1026209/139‑1 (MQ=255)
      ggggTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            <  1:604646/139‑1 (MQ=255)
                aCCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAg                                                                                  >  1:466326/1‑139 (MQ=255)
                  cTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            >  1:175139/1‑127 (MQ=255)
                  cTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            <  2:175139/127‑1 (MQ=255)
                    ggCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGatat                                                                              >  2:404669/1‑139 (MQ=255)
                      cGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            <  1:417098/123‑1 (MQ=255)
                      cGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            >  2:417098/1‑123 (MQ=255)
                                        cgagcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGata                                                                               <  1:563230/118‑1 (MQ=255)
                                        cgagcgGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGata                                                                               >  2:563230/1‑118 (MQ=255)
                                             gggCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGCTATTTa                                                                           >  1:679700/1‑117 (MQ=255)
                                             gggCAACGAATGGCGTTTGAGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGATATTTa                                                                           <  2:679700/117‑1 (MQ=255)
                                                cAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAAc                                                  >  2:540495/1‑139 (MQ=255)
                                                  aCGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAAccc                                                <  1:463457/139‑1 (MQ=255)
                                                     aaTGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCgg                                             <  1:404669/139‑1 (MQ=255)
                                                         gCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            <  1:597784/88‑1 (MQ=255)
                                                         gCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            >  2:597784/1‑88 (MQ=255)
                                                              tgttCAATAGCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGACGTATTACGTTAGTGCT‑TGTTTGAAAGCCGTCTGTATCAAGATATTTATCAGAACAATTAACCAGAAAGTTTCCCGGGAACATGGcc                                    <  2:130455/139‑1 (MQ=255)
                                                                                   tGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGata                                                                               >  1:1116099/1‑75 (MQ=255)
                                                                                   tGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGata                                                                               <  2:1116099/75‑1 (MQ=255)
                                                                                   tGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACaa               >  1:754345/1‑139 (MQ=255)
                                                                                         aGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            <  1:789918/56‑1 (MQ=255)
                                                                                         aGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            >  2:789918/1‑56 (MQ=255)
                                                                                           aaCCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCGCATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCt       >  1:713532/1‑139 (MQ=255)
                                                                                            aCCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCtt      <  1:540495/139‑1 (MQ=255)
                                                                                                gCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGtt  >  2:799621/1‑139 (MQ=255)
                                                                                                 cGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            >  1:647486/1‑48 (MQ=38)
                                                                                                 cGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            >  1:575158/1‑48 (MQ=38)
                                                                                                 cGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            <  2:575158/48‑1 (MQ=38)
                                                                                                 cGGATCAGCGTAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGt                                                                                            <  2:647486/48‑1 (MQ=38)
                                                                                                           tAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAAcccc                                               >  2:353477/1‑83 (MQ=255)
                                                                                                           tAATCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAATCAAAAAGAAAcccc                                               <  1:353477/83‑1 (MQ=255)
                                                                                                              tCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGta                                                                                       >  2:144695/1‑40 (MQ=38)
                                                                                                              tCGCCGTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGta                                                                                       <  1:144695/40‑1 (MQ=255)
                                                                                                                   gTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAg                                                                       <  2:891459/51‑1 (MQ=255)
                                                                                                                   gTATTCCGTTAGTGCGTT‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAg                                                                       >  1:891459/1‑51 (MQ=255)
                                                                                                                                   |                                                                                                        
TTGCAGGGGGTATATAACCTGGCGGGATTCATTACCACAGCGAGCGGGCAACGAATGGCGTTTGTGCAATATCTTTCTGGCTATGCAGTAGAACCTGCGGATCAGCGTAATCGCCGTATTCCGTTAGTGCG‑T‑TTTGAAAGCCGTTTGTATAAAGATATTTATCAGAACAATTAGTCAAAAAGAAACCCCGGCACATGGCCGGGGCTTCAGATTATTGACAAAGTGCGCTTTGTT  >  NC_000913/3330223‑3330456

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A