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 F104 I1 R1 35 102.1 2392160 96.4% 2306042 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA USA300TCH1516_ALE 1,440,085 G→T intergenic (‑45/+126) cspA_2 ← / ← USA300TCH1516_01338 Cold shock protein CspA/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*USA300TCH1516_ALE1,440,0850GT96.4% 244.4 / NA 87intergenic (‑45/+126)cspA_2/USA300TCH1516_01338Cold shock protein CspA/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (1/2);  new base T (27/54);  total (29/58)
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

CTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTAT  >  USA300TCH1516_ALE/1439947‑1440222
                                                                                                                                          |                                                                                                                                          
cTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCa                                                                                                                                          >  1:1064703/1‑141 (MQ=255)
 tGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCat                                                                                                                                         >  2:1174544/1‑141 (MQ=255)
    aaaaGGTACTATTACGTCATTTTCTCCTTCATCTTCGATAAAGCCGAAGCCTTTTTCAGCGTTAAACCATTTCACTGTACCTTGTTTCATAATCTGAAACCTCGAAGACTAAAATTCATTCAATATGCTTATTCGCATAtt                                                                                                                                      <  2:771105/141‑1 (MQ=255)
             gcaTACGTCATTTTCTCCTTCACCTCCGATAAAGCCGACTCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATGCGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAAt                                                                                                                            <  1:993018/139‑1 (MQ=255)
                  gctagttttCTCCTTCAACTTCGATAAAGCCCAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATg                                                                                                                       <  1:508170/136‑1 (MQ=255)
                  cctCATTTTCTCCTTCGAATTAGATAAAGCCGAATCCTTTTGCAGCGTCAAACCATTTAACTGTACCTTGTCTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATg                                                                                                                       <  1:77066/139‑1 (MQ=255)
                  cGTCATTTTCTCTTTCAACTTCGATAGAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATg                                                                                                                       <  1:510076/141‑1 (MQ=255)
                  cGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAACACCCCAAGACTAAAACTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATg                                                                                                                       <  1:464582/141‑1 (MQ=255)
                  cGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATg                                                                                                                       <  2:447386/141‑1 (MQ=255)
                      aTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCaaa                                                                                                                   <  2:685959/141‑1 (MQ=255)
                      aTTTTCTCCTTCAACTACAATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCCCAACCCTCCAAGACTAAAATTCATTCAATATGCTTATTAAAAAAAAAA‑AAAAAATACATGCaaa                                                                                                                   <  2:948960/141‑1 (MQ=255)
                            tcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCCATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCAc                                                                                                             >  2:575834/1‑141 (MQ=255)
                            tcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCAc                                                                                                             <  1:423148/141‑1 (MQ=255)
                             ccTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCAcc                                                                                                            >  1:476578/1‑140 (MQ=255)
                                  ttcTTCGATAAAGCCGTATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTTTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCATATTTCACTCAAat                                                                                                       <  2:407582/139‑1 (MQ=255)
                                  aaattCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTAATCACCCGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAat                                                                                                       <  1:569701/138‑1 (MQ=255)
                                  aaCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAat                                                                                                       <  2:878723/141‑1 (MQ=255)
                                  aaCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAat                                                                                                       <  1:176037/141‑1 (MQ=255)
                                  aaCTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAat                                                                                                       <  2:248705/141‑1 (MQ=255)
                                  aaCTTCGAGAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAat                                                                                                       <  1:508365/141‑1 (MQ=255)
                                  aaCTTAGATAAAGCAGAATCCTTTTTAAGCTTTAAACCATTTTACTGAACCTTGTTCCATAAACTGATACCACCAAAACTAAAATTTATTCAATATTCTTATCCTAAAAAAAA‑AAAAAATACATGCAAATTTCACTCaact                                                                                                       <  2:409274/141‑3 (MQ=255)
                                    cTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAatat                                                                                                     >  1:246121/1‑141 (MQ=255)
                                        gATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCtt                                                                                                 <  2:970836/141‑1 (MQ=255)
                                           acaGCCGAATCCTTGTTCCGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                                                                              <  2:214705/139‑1 (MQ=255)
                                           aacgCCTAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                                                                              <  2:279830/138‑1 (MQ=255)
                                           aaaGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTTCCTTGTTTCATAAACTGAACCACACAAGACTAAAATTCACTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                                                                              <  1:687571/141‑1 (MQ=255)
                                           aaaGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAATCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                                                                              <  1:687585/141‑1 (MQ=255)
                                           aaaGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGc                                                                                              >  1:609573/1‑141 (MQ=255)
                                                cGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                                                                                         <  2:1040449/141‑1 (MQ=255)
                                                cGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTCGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTGTTCTCATATTAC‑AAAAAATACATGCAAATTTCAGTCAAATATTCTTTGCAatat                                                                                         <  1:775424/141‑1 (MQ=255)
                                                cGAATCCTTTTTAAGCATTAAACCATTTAACTGTACCTTGTTTCATAATCTAAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTAAAAAAAAAA‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat                                                                                         <  2:1187826/141‑1 (MQ=255)
                                                    tCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaa                                                                                     >  1:893919/1‑141 (MQ=255)
                                                    tCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTCCAATATGGaa                                                                                     >  2:807817/1‑141 (MQ=255)
                                                    tCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGATTATTCGCATAGTAC‑AAAACAAACATCAAACTTTAACTCAAATATACTTTACAATATGGaa                                                                                     >  2:396629/1‑141 (MQ=255)
                                                     ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaat                                                                                    >  2:1007453/1‑141 (MQ=255)
                                                     ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaat                                                                                    >  2:643909/1‑141 (MQ=255)
                                                     ccTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaaa                                                                                    >  2:1053762/1‑140 (MQ=255)
                                                       tttttCAGCGTTAAACCATTTAACTGTACCCTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaataa                                                                                  <  2:86510/141‑1 (MQ=255)
                                                              gCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTg                                                                           <  2:326169/141‑1 (MQ=255)
                                                              gCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTg                                                                           <  2:137432/141‑1 (MQ=255)
                                                              gCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTg                                                                           <  2:924573/141‑1 (MQ=255)
                                                              gCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTg                                                                           <  1:56913/141‑1 (MQ=255)
                                                              gCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGTAATATGGAATAATCATCTg                                                                           <  1:889779/141‑1 (MQ=255)
                                                               cGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATTTGGAATAATCATCTGc                                                                          <  1:664112/141‑1 (MQ=255)
                                                               cGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTATAATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGc                                                                          <  2:324583/141‑1 (MQ=255)
                                                                gTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACTTCCAAGACTAAAGTGCATTCAATATGCTTATTCTAAACTAAC‑AAAAATGACATGATAATGTCACTCAAATATTCTTTGCAATACGGATTAATCCTATGCt                                                                         >  2:587861/1‑141 (MQ=255)
                                                                gTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGc                                                                          >  2:263774/1‑141 (MQ=255)
                                                                gTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCt                                                                         <  2:138888/141‑1 (MQ=255)
                                                                gTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTACTTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAGTTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCt                                                                         >  1:183012/1‑141 (MQ=255)
                                                                  tAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTACAAGACTAATATTCATTCAATATGCCCATCCTCAGATTAC‑TACAATTTCATTCAAAGTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTa                                                                       <  1:573290/141‑1 (MQ=255)
                                                                      ccATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACtt                                                                   >  2:346506/1‑141 (MQ=255)
                                                                        aTTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGt                                                                 <  1:267657/141‑1 (MQ=255)
                                                                          ttAACTGTGCCTTGTTCCATTATCTGAACCCTCCAAGACTAAAATTCCTTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtat                                                               <  2:1077449/141‑1 (MQ=255)
                                                                           tAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtatt                                                              >  1:899844/1‑141 (MQ=255)
                                                                            aaCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtatta                                                             <  1:239132/141‑1 (MQ=255)
                                                                            aaCTGTACCTTGGTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtatta                                                             <  2:162418/141‑1 (MQ=255)
                                                                             aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattat                                                            >  1:851266/1‑141 (MQ=255)
                                                                             aCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGtattat                                                            >  1:881189/1‑141 (MQ=255)
                                                                                gTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGt                                                         <  1:462571/141‑1 (MQ=255)
                                                                                  aCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCATTATGCTTATTCTCATTTTAT‑AAAAAATACATGCAAATTTCACTCAAATATTTTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTTTAGTga                                                       >  2:618446/1‑140 (MQ=255)
                                                                                   ccTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCa                                                      <  1:1058775/141‑1 (MQ=255)
                                                                                       gTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATtata                                                           <  2:650811/132‑1 (MQ=255)
                                                                                       gTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATtata                                                           >  1:650811/1‑132 (MQ=255)
                                                                                          tCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAATATACATGCAAATTTCACTCAAATAATCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatta                                               <  1:772009/141‑1 (MQ=255)
                                                                                            aTAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTCTTAcc                                             >  2:564114/1‑141 (MQ=255)
                                                                                               aTCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCaaa                                          <  1:852375/141‑1 (MQ=255)
                                                                                               aTCTGAAACCTACAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCaaa                                          <  1:284437/141‑1 (MQ=255)
                                                                                                tCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAt                                         >  2:1175568/1‑141 (MQ=255)
                                                                                                  tGAAACCTCCAAGACTAAAATTCATTCAATATACTTATTCTCATATTAC‑AAAAAATACACGCAAATTTCACTCAAATATTCTTTTCAAAATGGAACAATCATCTGCTTAACTTGTATTATAACGCAGTTATTACACAAtta                                       >  2:318312/1‑140 (MQ=255)
                                                                                                  tGAAACCTCCAAAACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTg                                       <  2:1175567/141‑1 (MQ=255)
                                                                                                   gAAACCTCCAAGACTAAAATTCATTCAATATGCTCATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGc                                      <  2:599215/141‑1 (MQ=255)
                                                                                                   gAAACCTCCAAGACAAAAAATCATTCAATAAGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCGTTGCAATATGGAATAATCATCTGCTTAACTCGTATTAGAGTGCAGCTATTACCAAATTGc                                      <  2:575319/141‑1 (MQ=255)
                                                                                                        ccccAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCACATTGcaatac                                 >  2:316862/3‑141 (MQ=255)
                                                                                                             aGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaatacaatca                            >  2:853697/1‑139 (MQ=255)
                                                                                                             aGACTAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACaataa                            >  2:81378/1‑141 (MQ=255)
                                                                                                                 tAAAATTCATTCAATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaa                        <  1:1040867/141‑1 (MQ=255)
                                                                                                                  aaacTTCGTACAAAAGGCTTATTCTCATATTAC‑AAAAAATACCTGCAAATTTCTCTCAAATATTTTTTGCAATATGGAATAATCTTCTGCCTAACTTGTATTATAGTTCAGTTATTCCCAAATTGCAATACAATAATaaaa                       <  2:198143/141‑1 (MQ=255)
                                                                                                                  aaaaTTCATCCAATATGCTTATTCTCATATAAA‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaa                       <  2:119063/141‑1 (MQ=255)
                                                                                                                       tcattcaATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAatat                  >  1:943644/1‑141 (MQ=255)
                                                                                                                          ttcaATATGCTTATTCTCATATTAC‑AAAAAAAACATTCAAATTTCACTCAAATATTCTTTGCAATATGTAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCa               <  1:1174544/141‑1 (MQ=255)
                                                                                                                          ttcaATATGCTTATTCACATATTAC‑AAAAAATACATACAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCa               >  1:711252/1‑141 (MQ=255)
                                                                                                                           tcaATATGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCAt              <  2:126416/141‑1 (MQ=255)
                                                                                                                                 tGCTTATTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAGAAAATATTCATTTAATc        <  1:547264/141‑1 (MQ=255)
                                                                                                                                 tGCTTATTCTCAAATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATc        <  1:1041513/141‑1 (MQ=255)
                                                                                                                                      aTTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatta   <  2:568399/141‑1 (MQ=255)
                                                                                                                                      aTTCTCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAatta   <  2:828973/141‑1 (MQ=255)
                                                                                                                                       ttCTCAAATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAattat  <  1:189031/141‑1 (MQ=255)
                                                                                                                                          |                                                                                                                                          
CTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTAC‑AAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTAT  >  USA300TCH1516_ALE/1439947‑1440222

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