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
A17 F172 I0 R1 42 33.2 716278 96.8% 693357 139.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 1,232,465 G→C 100% A124P (GCG→CCG)  USA300HOU_1157 → non‑specific serine/threonine protein kinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP0007301,232,4650GC100.0% 104.3 / ‑6.5 35A124P (GCG→CCG) USA300HOU_1157non‑specific serine/threonine protein kinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base C (15/19);  minor base A (1/0);  total (16/19)
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.

GAAGATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATGCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAGACTAATCA  >  CP000730/1232330‑1232598
                                                                                                                                       |                                                                                                                                     
gaagaTGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATACGCa                                                                                                                                   >  2:101867/1‑140 (MQ=255)
   gaTGACTGTTACTACTTAATACTGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGa                                                                                                                                <  1:152351/140‑1 (MQ=255)
     tGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGCATATGGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTGATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGata                                                                                                                              >  1:206430/1‑140 (MQ=255)
       aCTGTTACTACTTAGTAAAGGAATAAAACGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATg                                                                                                                            <  1:278651/140‑1 (MQ=255)
        cTGTAAATACGTAGCAATGGAATATATCGAAGGTCCGACATTGTCTGAGTATATGGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCACTAAACATCCGCACGATATGc                                                                                                                           <  1:223177/140‑1 (MQ=255)
         tGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCg                                                                                                                          >  1:297662/1‑140 (MQ=255)
              ctactTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTg                                                                                                                     <  2:311001/140‑1 (MQ=255)
                        aTGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAgaga                                                                                                           >  1:72023/1‑140 (MQ=255)
                             atatatCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTa                                                                                                      >  1:181520/1‑140 (MQ=255)
                               atatCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGACATTCAGTGTTGACAACGCGATTAATTTTAGGAATCAGATATTGGATGGCATTAGACATCCGGTTGAACTGCTTATGGTAAATTGTGCTATTAAg                                                                                                    >  2:171008/1‑140 (MQ=255)
                                tatCGAAGGTCCGACTTTGTCAGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGc                                                                                                   <  1:289638/140‑1 (MQ=255)
                                    gAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAAATATTAAGCcaca                                                                                               >  1:115094/1‑140 (MQ=255)
                                       ggTCCGACTTTGTCGGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAGCATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACaaaa                                                                                            <  2:228572/140‑1 (MQ=255)
                                           cGACTTTGTCTGAGTAGATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGGCACAAAatata                                                                                        >  1:212262/1‑140 (MQ=255)
                                                   tCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCg                                                                                                                          >  2:220486/1‑98 (MQ=255)
                                                   tCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCg                                                                                                                          <  1:220486/98‑1 (MQ=255)
                                                         tataTTGAAAGTCATGGGCCATAAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCaa                                                                          <  1:320865/140‑1 (MQ=255)
                                                         aataataaaaGTCAAGGGCCAATAAGTATTGACACAGCAATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCaa                                                                          <  1:356160/133‑1 (MQ=255)
                                                                     cATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGaa                                                              >  1:22104/1‑140 (MQ=255)
                                                                     cATGGGCCATTAAGGGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGaa                                                              <  1:60832/140‑1 (MQ=255)
                                                                        gggCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAat                                                           >  1:149713/1‑140 (MQ=255)
                                                                          gCCATTAAGTGTTGACACTGAGATTAACTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAatat                                                         <  2:217468/140‑1 (MQ=255)
                                                                          gCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAatat                                                         >  1:269569/1‑140 (MQ=255)
                                                                                  gtgtTGGCACAGCGATTAATTTTACGAATCAAATATTGGAGGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGAtttt                                                 <  2:178382/140‑1 (MQ=255)
                                                                                            aGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTa                                       >  1:255486/1‑140 (MQ=255)
                                                                                              ccaTTAATTTTACGAAACAAATATTGGATGGAATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTaaa                                     <  1:153368/138‑1 (MQ=255)
                                                                                               gATTAATTTTACGAATCAAATATTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAg                                    >  2:145942/1‑140 (MQ=255)
                                                                                                        tACGAATTAATAATTGGATGGCATTAAACTTCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTg                           <  2:187554/140‑1 (MQ=255)
                                                                                                               cAAATATTGGATGGCATTAAACATCCGCATTATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTc                    <  1:86703/140‑1 (MQ=255)
                                                                                                                  atatTGGATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCttt                 <  2:122884/140‑1 (MQ=255)
                                                                                                                       ggATGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTc            <  2:72023/140‑1 (MQ=255)
                                                                                                                         aTGGCATTAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAg          >  2:94277/1‑140 (MQ=255)
                                                                                                                               ttAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAGACTAAt    <  2:22104/140‑1 (MQ=255)
                                                                                                                                tAAACATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAGACTAATc   >  1:75372/1‑140 (MQ=255)
                                                                                                                                 aaaCATCCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAGACTAATCa  <  2:122422/140‑1 (MQ=255)
                                                                                                                                       |                                                                                                                                     
GAAGATGACTGTTACTACTTAGTAATGGAATATATCGAAGGTCCGACTTTGTCTGAGTATATTGAAAGTCATGGGCCATTAAGTGTTGACACAGCGATTAATTTTACGAATCAAATATTGGATGGCATTAAACATGCGCATGATATGCGTATTGTACATAGAGATATTAAGCCACAAAATATATTAATTGACAGCAATAAAACGTTGAAAATATTTGATTTTGGAATTGCTAAAGCTTTAAGTGAGACGTCTTTAACTCAGACTAATCA  >  CP000730/1232330‑1232598

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