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
A13 F121 I0 R1 43 32.8 695000 96.9% 673455 140.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA CP000730 849,263 C→A 41.9% A130E (GCA→GAA)  USA300HOU_0794 → ATP‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*CP000730849,2630CA41.9% 18.8 / 37.7 36A130E (GCA→GAA) USA300HOU_0794ATP‑binding protein
Reads supporting (aligned to +/- strand):  ref base C (13/8);  new base A (5/10);  total (18/18)
Fisher's exact test for biased strand distribution p-value = 1.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.00e-01

AAGTCAAAAGTGAAAGTGACGTCATCATTGATGTTATGTTTTTAGAAGCAAGTACTGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGTTATCACCTAAAGAATTAAAAGAACGCATTCGTCGATACTATGAAGATGAAGAGTTTG  >  CP000730/849128‑849391
                                                                                                                                       |                                                                                                                                
aaGTCAAAAGTGAAAGTGACGTCATCATTGATGTTATGTTTTTAGAAGCAAGTACTGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTa                                                                                                                             >  1:258551/1‑141 (MQ=255)
        agtgaaagtgaCGTCATTATTGATGTTATGTTTTTAGAAGCAAGTACTGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGAAATTAATGATGAg                                                                                                                     <  1:287821/141‑1 (MQ=255)
             aagtgaCGTCATCAGTGATGTTATGTTTTTAGAAGCAAGTACTGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCgaga                                                                                                                >  1:225452/1‑141 (MQ=255)
              agtgaCGTCATCATTGATGTTATGTTTTTAGAAGCAAGTACTGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGagag                                                                                                               >  2:266755/1‑141 (MQ=255)
              agtgaCGTCATCATTGATGTTATGTTTTTAGAAGCAAGTACTGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCATTTGATGGAACAAGGTAAAAGATCGTTGATAAATGCAAGTCATGATAAGAGaaag                                                                                                               >  2:218980/1‑141 (MQ=255)
               gtgaCGTCATCATTGATGTTATGTTTTTAGAAGCAAGTACTGAAAAATTAATTTCAAGATATAAGGAAAAGCGTCGTGCACATCCTTTGATGGAGCAAGGTAAAAGATCGTTAATCAATGAAATTAATGATGAGCgagacc                                                                                                              >  2:9766/1‑139 (MQ=255)
                       atcatTGATGTTATGTTTTTAGAAGCAAGTACTGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGAAATTAATGATGAGCGAGAGCATTTGtct                                                                                                      <  1:245994/141‑1 (MQ=255)
                                  tatgttTTTCGAAGCAAGTACTGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGAAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAg                                                                                           <  1:25549/141‑1 (MQ=255)
                                        tttAGAAGCAAGGACTGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGAAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGc                                                                                     <  2:82900/141‑1 (MQ=255)
                                                 aaGTACTGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGAAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGt                                                                            <  1:14458/141‑1 (MQ=255)
                                                 aaGTACTGAAAAATTAATCTCAAGATAACAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATTAATGAAATTAATGATGTGCGAGAGTATTTGTCTCAAATTAGAAGTATAGCTAATTTTGt                                                                            <  1:14464/141‑1 (MQ=255)
                                                   gTACTGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATAAGTTTGATTTTAGAAGTATAGCTGATTTTGTta                                                                          <  1:253602/141‑1 (MQ=255)
                                                       tGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGa                                                                      <  1:341160/141‑1 (MQ=255)
                                                       ggcaaaaTTAATTTAAAGATTTAGGGAAACGCCTCGTGCACATCCTTTGATGGAACGAGGTAAAAGATCGTTAATCAATTCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGa                                                                      <  2:52524/138‑1 (MQ=255)
                                                        gAAAAATTAATTTCAAGATATAAGGAAACGCGACGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCACATCTCTCAAATTAGAAGTATAGCGACTTTTGGTATAGaa                                                                     >  2:195179/1‑140 (MQ=255)
                                                        gAAAAATTAAGTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGAt                                                                     >  1:249844/1‑141 (MQ=255)
                                                           aaaTTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAAGAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGAtact                                                                  >  1:264651/1‑141 (MQ=255)
                                                             attaattTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGAAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGAtactac                                                                >  2:142141/1‑141 (MQ=255)
                                                              ttaattTCAAGATATTAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAGAGATCGTTAATCAATGAAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACa                                                               <  1:107266/141‑1 (MQ=255)
                                                                aattTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACaaa                                                             <  2:25091/141‑1 (MQ=255)
                                                                  tttCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGAAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGt                                                           <  2:271078/141‑1 (MQ=255)
                                                                   ttCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGAAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGtt                                                          >  2:132060/1‑141 (MQ=255)
                                                                    tCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATTGAACAAGGTAAAAGATCGTTAATCAATGAAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTAAAAAGTTa                                                         >  2:109344/1‑141 (MQ=255)
                                                                           ataAGGAAACGCGGCGGGCACCTCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGTTATCACCTa                                                  <  1:309823/141‑1 (MQ=255)
                                                                            taAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGAAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGTTATCACCTaa                                                 >  2:314038/1‑141 (MQ=255)
                                                                             aaagAAACGCGGCGTGCACATCCTTTGATGGAACAACGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGGGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATTCAACAAAGTTATCACCaaaa                                                >  2:105508/4‑141 (MQ=255)
                                                                             aaGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGTTATCACCTaaa                                                <  1:320221/141‑1 (MQ=255)
                                                                             aaGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGAGCGTTAAGCAATGCAATTTAGGATGAGCGATAGCATTTGTTTCAAATTAGAAGTATAGCTAATTTTGTTATAGATTCTACAAAGTTATGACCTaaa                                                >  2:135335/1‑141 (MQ=255)
                                                                                         cgtGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGTTATAACCGCAAGAATCAAAAGaa                                    >  2:60949/1‑141 (MQ=255)
                                                                                                     ttGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGTTATCACCTAAAGAATTAAAAGAACGCATTCGTCGa                        >  1:3315/1‑141 (MQ=255)
                                                                                                               aaGGTAAAACATCGTTAATCAATGAAAGTAATGATGAGCGAGAGCCCCTGAATCAAATCAGAAGTATAGCTAATTGTGTTATAGATACTACAAAGTTATCACCTAAAGAATTAAAAGAACGCATTCGTCGATACTatgaag              <  1:9766/141‑1 (MQ=255)
                                                                                                                     aaaGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGTCACCACCTAAAGAATTAAAAGAACGCATTCGTCGATACTatgaagatgaag        >  1:191439/1‑141 (MQ=255)
                                                                                                                        gATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGTTATCACCTAAAGAATTAAAAGAACGCATTCGTCGATACTATGAAGATGAAGAGt     <  2:264651/141‑1 (MQ=255)
                                                                                                                         aTCGTTAATCAATGCAATGAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGTTATCACCTAAAGAATTAAAAGAACGCATTCGTCGATACTATGAAGATGAAGAGtt    <  2:158993/141‑1 (MQ=255)
                                                                                                                           cgctAATCAATGAAATTAATGATGAGCGAGAGCATTTGTCGCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGTTATCACCTAAAGAATTAAAAGAACGCATTCGTCGATACTATGAAGATGAAGAGTTTg  <  2:290319/138‑1 (MQ=255)
                                                                                                                           cGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGTTATCACCTAAAGAATTAAAAGAACGCATTCGTCGATACTATGAAGATGAAGAGTTTg  >  1:261442/1‑141 (MQ=255)
                                                                                                                                       |                                                                                                                                
AAGTCAAAAGTGAAAGTGACGTCATCATTGATGTTATGTTTTTAGAAGCAAGTACTGAAAAATTAATTTCAAGATATAAGGAAACGCGTCGTGCACATCCTTTGATGGAACAAGGTAAAAGATCGTTAATCAATGCAATTAATGATGAGCGAGAGCATTTGTCTCAAATTAGAAGTATAGCTAATTTTGTTATAGATACTACAAAGTTATCACCTAAAGAATTAAAAGAACGCATTCGTCGATACTATGAAGATGAAGAGTTTG  >  CP000730/849128‑849391

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