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 F18 I0 R1 32 69.1 1533550 96.6% 1481409 141.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA USA300TCH1516_ALE 1,513,930 A→T 100% L413F (TTA→TTT)  USA300HOU_RS07375 → hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,513,9300AT100.0% 190.8 / NA 57L413F (TTA→TTT) USA300HOU_RS07375hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base T (29/28);  total (29/28)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TAATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  USA300TCH1516_ALE/1513792‑1514064
                                                                                                                                           |                                                                                                                                      
tAATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTAt                                                                                                                                      >  2:626738/1‑141 (MQ=255)
        ttGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAg                                                                                                                              <  1:599475/141‑1 (MQ=255)
            atgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTAGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCAGTCATAATATGTTTTATTGTATTAGGatt                                                                                                                          >  1:434707/1‑141 (MQ=255)
              ttatCGCTTTATTAGTAGCCATTGGCATAGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGattat                                                                                                                        <  1:46347/140‑1 (MQ=255)
                    cTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGc                                                                                                                  <  1:96382/141‑1 (MQ=255)
                       gatgagtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCat                                                                                                               <  2:763002/137‑1 (MQ=255)
                         ttaGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGCTTTATTGTATTAGGATTATTAATGCCatta                                                                                                             >  2:485178/1‑141 (MQ=255)
                         ttaGTAGCAATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCAAATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCatta                                                                                                             <  2:41826/141‑1 (MQ=255)
                            gtggCCATGGGCATGGGGATTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTATCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTCGGATTAGTAATGCCATTAttt                                                                                                          <  2:526254/138‑1 (MQ=255)
                            gtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTAttt                                                                                                          >  2:166557/1‑141 (MQ=255)
                            gtagCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTAttt                                                                                                          <  2:279455/141‑1 (MQ=255)
                              agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                                        <  2:14869/141‑1 (MQ=255)
                              agCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTgg                                                                                                        <  2:14797/141‑1 (MQ=255)
                                  aTTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTa                                                                                                    >  1:74312/1‑141 (MQ=255)
                                   tcgggagggggTTGGTCGCTTGGATAAGGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCGATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                   <  2:54433/134‑1 (MQ=255)
                                   taggaaTGCGGTTGGTCTCCTGGATAAAGCGTACAAAAAATACTGTCATAAAAGTACGACAAAT‑AATAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTAt                                                                                                   <  2:242301/136‑1 (MQ=255)
                                    tGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACC‑TATCGACTCAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATc                                                                                                  <  1:557709/141‑1 (MQ=255)
                                     ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                 >  1:61238/1‑141 (MQ=255)
                                     ggCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACAACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCa                                                                                                 >  2:142984/1‑141 (MQ=255)
                                      gCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGTTTATTTATGCCATTATTTGGATTATCat                                                                                                >  1:440811/1‑140 (MQ=255)
                                       cATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACt                                                                                               >  1:659875/1‑141 (MQ=255)
                                        aTGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACtt                                                                                              >  1:621405/1‑141 (MQ=255)
                                         tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTCGGATTATTAATGCCATTATTTGGCTTATCACTTa                                                                                             >  1:375956/1‑141 (MQ=255)
                                         tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTa                                                                                             >  2:596102/1‑141 (MQ=255)
                                         tGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGGATTAGGATTATTAATGCCATTATTTGGATTATCACttt                                                                                             >  2:275062/1‑140 (MQ=255)
                                           gggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCCCATCG‑CGGAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATc                                                                                           >  1:368372/1‑141 (MQ=255)
                                              gttGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCtt                                                                                        <  2:229624/140‑1 (MQ=255)
                                               ttGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTTTCACTTATCAttt                                                                                       >  2:297406/1‑140 (MQ=255)
                                                 gTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTa                                                                                     >  2:239537/1‑141 (MQ=255)
                                                  tctcTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAt                                                                                    <  2:117419/141‑1 (MQ=255)
                                                  tctcTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAt                                                                                    <  2:688744/141‑1 (MQ=255)
                                                  tctcTTAGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTAt                                                                                    <  2:679036/141‑1 (MQ=255)
                                                          aTAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGGCATTGTTTGGGTTATCCCTTATCCTTGTTTTTATAAtt                                                                            >  1:234712/1‑141 (MQ=255)
                                                           tAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTg                                                                           <  1:674998/141‑1 (MQ=255)
                                                             aaGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGaa                                                                         >  2:725498/1‑141 (MQ=255)
                                                              aGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAt                                                                        >  1:629393/1‑141 (MQ=255)
                                                               gCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                       >  2:106906/1‑141 (MQ=255)
                                                                      aaaaaTACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAAtatta                                                                >  2:363200/1‑141 (MQ=255)
                                                                       aaaaTACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTTTATTTGTCATTGGTTTAAtattgt                                                               >  1:245155/1‑139 (MQ=255)
                                                                                     aaaGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGAtcgt                                                 <  1:626738/141‑1 (MQ=255)
                                                                                       aGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTTAATTAATATTATATATTAAAAgtcgtct                                               >  2:230390/1‑140 (MQ=255)
                                                                                          aCCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTgt                                            >  1:686452/1‑140 (MQ=255)
                                                                                            cacaTCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTa                                          <  1:273023/141‑1 (MQ=255)
                                                                                             ccaTCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTaa                                         <  1:360371/140‑1 (MQ=255)
                                                                                             aaaacg‑cgAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTaa                                         <  2:711769/137‑1 (MQ=255)
                                                                                                     gTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaataa                                  >  1:647525/1‑141 (MQ=255)
                                                                                                       aaaaaaaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATg                                <  1:623726/141‑1 (MQ=255)
                                                                                                        aaaaaaCCAGCATCTATATCACTCAGAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATTATTGATTTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGc                               >  1:13494/1‑141 (MQ=255)
                                                                                                         aaaacCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCa                              <  1:3371/141‑1 (MQ=255)
                                                                                                            aaCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACtt                           <  2:629393/141‑1 (MQ=255)
                                                                                                                aGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAg                       >  1:346993/1‑141 (MQ=255)
                                                                                                                 gCATCTATATCACTCATAATATGTTTTATTGTATGAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGAACTTaaaat                      >  2:579636/1‑139 (MQ=255)
                                                                                                                  cATCTATATCACTCATAATATGTTTTATTGTATTAGGAGTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGtt                     <  1:80827/141‑1 (MQ=255)
                                                                                                                   aTCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGttt                    <  2:150552/141‑1 (MQ=255)
                                                                                                                          tCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTg             >  1:655596/1‑141 (MQ=255)
                                                                                                                                 taataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAt      <  1:246790/141‑1 (MQ=255)
                                                                                                                                     ttGTTTTATTGTATTAGGATTATTACTTCCATTATTTTTATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAc  <  1:474528/140‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                      
TAATTTATTTGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCG‑CGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTTAC  >  USA300TCH1516_ALE/1513792‑1514064

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ 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