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
A21 F39 I0 R1 217 77.2 2771496 98.2% 2721609 143.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,085,419 A→G 10.0% V36A (GTG→GCG)  yeeE ← UPF0394 family inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,085,4190AG10.0% 133.9 / 7.0 50V36A (GTG→GCG) yeeEUPF0394 family inner membrane protein
Reads supporting (aligned to +/- strand):  ref base A (30/15);  new base G (3/2);  total (33/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.41e-01

GATATACCCACCTATAACAGTACCAAGCCACGGGAACGCCCCGGCTTCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGAATGTTAATGAGGAAATTATTCAT  >  NC_000913/2085277‑2085567
                                                                                                                                              |                                                                                                                                                    
gATATACCCACCTATAACAGTACCAAGCCACGGGAACGCCCCGGCTTCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCGCGatat                                                                                                                                                <  1:241334/149‑1 (MQ=255)
         aCCTATAACAGTACCAAGCCACGGGAACGCCCCGGCTTCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATcgc                                                                                                                                       >  4:109505/1‑149 (MQ=255)
                       cAAGCCACGGGAACGCCCCGGCTTCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTc                                                                                                                         >  1:402263/1‑149 (MQ=255)
                       cAAGCCACGGGAACGCCCCGGCTTCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTc                                                                                                                         <  4:225890/149‑1 (MQ=255)
                                   aCGCCCCGGCTTCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCTCCTGTCAGGCAAAAACGc                                                                                                             <  4:362542/149‑1 (MQ=255)
                                   aCGCCCCGGCTTCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGc                                                                                                             <  3:46237/149‑1 (MQ=255)
                                       cccGGCTTCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAGGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCAc                                                                                                         >  1:307004/1‑149 (MQ=255)
                                       cccGGCTTCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCAc                                                                                                         >  4:238431/1‑149 (MQ=255)
                                       cccGGCTTCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCAc                                                                                                         >  3:577837/1‑149 (MQ=255)
                                           gCTTCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTg                                                                                                     >  2:90889/1‑149 (MQ=255)
                                              tCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCAt                                                                                                  >  3:447964/1‑149 (MQ=255)
                                                gTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGa                                                                                                >  1:65353/1‑149 (MQ=255)
                                                 tAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGAc                                                                                               >  3:549849/1‑149 (MQ=255)
                                                 tAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGAc                                                                                               >  2:643247/1‑149 (MQ=255)
                                                    gTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACaaa                                                                                            >  3:265835/1‑149 (MQ=255)
                                                       aGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATcc                                                                                         >  4:315062/1‑149 (MQ=255)
                                                         tAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCca                                                                                       <  4:105595/149‑1 (MQ=255)
                                                              ccGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCaga                                                                                  >  1:642121/1‑149 (MQ=255)
                                                                           cGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTa                                                                     <  1:543998/149‑1 (MQ=255)
                                                                            gCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAg                                                                    >  4:86758/1‑149 (MQ=255)
                                                                             cAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGc                                                                   <  3:425920/149‑1 (MQ=255)
                                                                               aaaaCGCCCACGCTTTGTACCGAAATTGGAATCAGCAAGGCGTAAAACATGAGACTATTTTTCACGATATACATATAACGAAAACCACATATCAGGCAAAAACTCACACTCTGCATAACAAATAACACAACAGCCCCACAAAAAAGccc                                                                 >  4:622632/1‑149 (MQ=255)
                                                                                aaaCCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCg                                                                >  4:443904/1‑149 (MQ=255)
                                                                                aaaCCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCg                                                                >  3:503602/1‑149 (MQ=255)
                                                                                  aCCCCCACGCTTTGTACCGAAATTGCAATCAGCAGGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCt                                                              <  2:307004/149‑1 (MQ=255)
                                                                                       cACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCca                                                                                       >  4:631107/1‑119 (MQ=255)
                                                                                       cACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCca                                                                                       <  3:631107/119‑1 (MQ=255)
                                                                                            tttGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCAtt                                                    <  4:187850/149‑1 (MQ=255)
                                                                                               gTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGaa                                                 <  3:343161/149‑1 (MQ=255)
                                                                                                 aCCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGaaaa                                               >  2:666361/1‑149 (MQ=255)
                                                                                                        ttGCAATCCGCAAGGCGTAAAACATGCGATTATTTTTCACGATATAAATATCGCGAAAAAAACTTGTAAGGCAAAAACGTCCACGCTGCATGACAAATCCCAGCAGAGCACACCAACTTAGCCCGCTTAATATCAATAAAAACATaaac                                        >  2:370696/1‑148 (MQ=255)
                                                                                                        ttGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAaat                                        <  4:537629/149‑1 (MQ=255)
                                                                                                           cAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAaattaa                                     <  4:447964/149‑1 (MQ=255)
                                                                                                            aaTCAGCAAGGCGTAAAACATGCGATTATTTTTCACGTGATACATATCGCGAAAACCACCTGTCACGCAAAAACGCCCACGCTGCCTGACAAATCCCATCAGAGCACCACAAACTAGCCCGATTATTATCATTGCAAACATAaattaat                                    >  2:294291/1‑149 (MQ=255)
                                                                                                            aaTCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAaattaat                                    >  2:174649/1‑149 (MQ=255)
                                                                                                            aaTCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAaattaat                                    >  4:669099/1‑149 (MQ=255)
                                                                                                                aGCAAGGCGTACAACATGCGATTATTTTTCACGATATACATGTCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTACCCCGCTTAATATCATTGAAAACATAAAttaattaaa                                >  4:39093/1‑148 (MQ=255)
                                                                                                                   aaGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAg                             >  1:328123/1‑149 (MQ=255)
                                                                                                                    aGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGa                            >  4:30002/1‑149 (MQ=255)
                                                                                                                         tAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGAAt                       <  1:274672/149‑1 (MQ=255)
                                                                                                                         tAAAACATGCGATTATTTTTCACGATATACATAACGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGaac                       <  4:538891/149‑2 (MQ=255)
                                                                                                                               aTGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGAATGTTAAt                 >  1:135826/1‑149 (MQ=255)
                                                                                                                                    attattTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGAATGTTAATGAGGa            >  1:189164/1‑149 (MQ=255)
                                                                                                                                      tggttttCGCGATATGTATATCGTGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGAATGTTAATGAGGaaa          >  4:345522/4‑149 (MQ=255)
                                                                                                                                        tttttCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGAATGTTAATGAGGAAatt        <  3:320198/149‑1 (MQ=255)
                                                                                                                                        tttttCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGAATGTTAATGAGGAAatt        >  1:62968/1‑149 (MQ=255)
                                                                                                                                         ttttCGCGATATGTATATCGTGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGAATGTTAATGAGGAAatta       >  4:201715/1‑149 (MQ=255)
                                                                                                                                           ttCGCGATATGTATATCGTGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGAATGTTAAt                 >  4:362031/1‑137 (MQ=255)
                                                                                                                                           ttCGCGATATGTATATCGTGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGAATGTTAAt                 <  3:362031/137‑1 (MQ=255)
                                                                                                                                             cACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATAATTGAAAACATAAATTAATTAACCAGATGAATGTTAATGAGGAAATTATTCa   >  2:589397/1‑149 (MQ=255)
                                                                                                                                              aCGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGAATGTTAATGAGGAAATTATTCAt  <  4:265835/149‑1 (MQ=255)
                                                                                                                                              |                                                                                                                                                    
GATATACCCACCTATAACAGTACCAAGCCACGGGAACGCCCCGGCTTCGTAAGTCAGTAGGCCCGCCTGAATTAACGCAAAAACCCCCACGCTTTGTACCGAAATTGCAATCAGCAAGGCGTAAAACATGCGATTATTTTTCACGATATACATATCGCGAAAACCACCTGTCAGGCAAAAACGCCCACGCTGCATGACAAATCCCAGCAGAGCACCACAAATTAGCCCGCTTAATATCATTGAAAACATAAATTAATTAACCAGATGAATGTTAATGAGGAAATTATTCAT  >  NC_000913/2085277‑2085567

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A