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
A11 F142 I1 R1 99 64.8 3148104 96.3% 3031624 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,989,886 T→A D5V (GAT→GTT)  yqeL ← uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,989,8860TA91.3% 227.6 / 9.0 69D5V (GAT→GTT) yqeLuncharacterized protein
Reads supporting (aligned to +/- strand):  ref base T (2/4);  new base A (30/33);  total (32/37)
Fisher's exact test for biased strand distribution p-value = 6.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

AAAATAGATAACAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGATCAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATGAGTCGAACTCGACATTCATCTTA  >  NC_000913/2989790‑2989983
                                                                                                |                                                                                                 
aaaaTAGATAACAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGATCaa                                                                                                >  2:1015973/1‑100 (MQ=255)
 aaaTAGATAACAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGaacaac                                                                                               <  1:133793/100‑1 (MQ=255)
  aaTAGATAACAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAacaaca                                                                                              <  2:96854/100‑1 (MQ=255)
  aaTAGATAACAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAacaaca                                                                                              >  1:1253341/1‑100 (MQ=255)
      gATAACAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCtt                                                                                          >  2:571275/1‑100 (MQ=255)
        tAACAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGATCAACATCTTTc                                                                                        >  2:1509073/1‑100 (MQ=255)
        tAACAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTc                                                                                        <  2:855122/100‑1 (MQ=255)
         aaCAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCa                                                                                       >  2:1010618/1‑100 (MQ=255)
          aCAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCAt                                                                                      >  2:1001237/1‑100 (MQ=255)
          aCAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCAt                                                                                      >  1:9430/1‑100 (MQ=255)
           cAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCAtt                                                                                     >  2:1553516/1‑100 (MQ=255)
            aaaaaGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCAtt                                                                                     <  1:191529/99‑1 (MQ=255)
             aaaaGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCAtttt                                                                                   <  1:102217/100‑1 (MQ=255)
             aaaaGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCAtttt                                                                                   <  2:1452027/100‑1 (MQ=255)
               aaGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAg                                                                                 <  1:1553526/100‑1 (MQ=255)
               aaGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAg                                                                                 <  2:102410/100‑1 (MQ=255)
                  aTGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACa                                                                              <  2:9430/100‑1 (MQ=255)
                    ggAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACAtc                                                                            >  1:988777/1‑100 (MQ=255)
                       aCCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTcc                                                                         >  2:210693/1‑100 (MQ=255)
                        ccTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCt                                                                        >  1:1202305/1‑100 (MQ=255)
                          tCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTg                                                                      >  2:535251/1‑100 (MQ=255)
                          tCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTg                                                                      <  1:571278/100‑1 (MQ=255)
                          tCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTg                                                                      <  1:303386/100‑1 (MQ=255)
                           cGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGc                                                                     <  2:327126/100‑1 (MQ=255)
                           cGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGc                                                                     >  1:518188/1‑100 (MQ=255)
                             ttAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCaa                                                                   <  1:608791/100‑1 (MQ=255)
                               aaTCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATg                                                                 <  2:136180/100‑1 (MQ=255)
                               aaTCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATg                                                                 >  2:1187402/1‑100 (MQ=255)
                                 tCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTa                                                               >  1:902153/1‑100 (MQ=255)
                                    tAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTaaaa                                                            >  1:163220/1‑100 (MQ=255)
                                     aaaaCAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGATCAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAat                                                           <  1:1394818/100‑1 (MQ=255)
                                         cAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCa                                                       >  2:1002727/1‑100 (MQ=255)
                                          aaTAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCAt                                                      <  1:264860/100‑1 (MQ=255)
                                          aaTAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCAt                                                      <  1:1474174/100‑1 (MQ=255)
                                           aTAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAGAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCAt                                                      <  1:1465714/99‑1 (MQ=255)
                                            tAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGt                                                    <  2:518185/100‑1 (MQ=255)
                                            tAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGt                                                    <  1:169377/100‑1 (MQ=255)
                                            tAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGt                                                    >  2:1416576/1‑100 (MQ=255)
                                              aaaTTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTAt                                                  >  1:62360/1‑100 (MQ=255)
                                               aaTTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATc                                                 <  2:902145/100‑1 (MQ=255)
                                                ctcttccgatctcGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATca                                                <  1:1420055/91‑1 (MQ=255)
                                                aTTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTTGACATCTCCTTGCAATGTAAAATATCATGTATca                                                <  1:228224/100‑1 (MQ=255)
                                                   aaaTATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATcaaca                                             <  2:416162/100‑1 (MQ=255)
                                                   aaaTATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATcaaca                                             <  1:1516536/100‑1 (MQ=255)
                                                     atatTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCaacaac                                           >  1:1151182/1‑100 (MQ=255)
                                                          ctcGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGATCAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTg                                      <  1:116051/100‑1 (MQ=255)
                                                          ctcGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTCCAATGTAAAATATCATGTATCAACAACATCTg                                      <  1:1490449/100‑1 (MQ=255)
                                                           tcGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTgg                                     <  1:807440/100‑1 (MQ=255)
                                                           tcGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTgg                                     >  1:121401/1‑100 (MQ=255)
                                                            cGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGt                                    >  2:242850/1‑100 (MQ=255)
                                                              cAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTg                                   <  2:696000/99‑1 (MQ=255)
                                                              cAGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGc                                  <  2:137769/100‑1 (MQ=255)
                                                               aGTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCa                                 >  1:1396366/1‑100 (MQ=255)
                                                                gTATATGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCaa                                >  2:275626/1‑100 (MQ=255)
                                                                  atatGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAAt                              <  1:721251/100‑1 (MQ=255)
                                                                    atGGCAGTTTAAAGCATCAAAGCTTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAAAGTAAAATATCCTGTATCAACCACATCTGGTGCAAAt                              >  2:28437/1‑98 (MQ=255)
                                                                    atGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATcc                            <  2:608669/100‑1 (MQ=255)
                                                                     tGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCa                           >  1:1261935/1‑100 (MQ=255)
                                                                     tGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCa                           >  2:648157/1‑100 (MQ=255)
                                                                     tGGCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCa                           >  2:1559193/1‑100 (MQ=255)
                                                                       gtaGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATg                         <  2:950933/98‑1 (MQ=255)
                                                                       gCAGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATg                         >  1:1153126/1‑100 (MQ=255)
                                                                         aGTCTAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATGAg                       <  1:1505273/100‑1 (MQ=255)
                                                                             tAAAGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATGAGTCGa                   >  2:789975/1‑100 (MQ=255)
                                                                                aGCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATGAGTCGAACt                >  1:29016/1‑100 (MQ=255)
                                                                                 gCATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATGAGTCGAACTc               <  1:1455421/100‑1 (MQ=255)
                                                                                  cATCAAAGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATGAGTCGAACTCg              <  1:644497/100‑1 (MQ=255)
                                                                                   aTCAAAGATTTGATCAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATGAGTCGAACTCGa             <  1:1509083/100‑1 (MQ=255)
                                                                                      aaaGATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATGAGTCGAACTCGACAt          >  1:262799/1‑100 (MQ=255)
                                                                                         gATTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATGAGTCGAACTCGACATTCa       <  2:267997/100‑1 (MQ=255)
                                                                                          aTTTGAACAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATGAGTCGAACTCGACATTCAt      >  1:960931/1‑100 (MQ=255)
                                                                                              gATCAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATGAGTCGAACTCGACATTCATCTTa  <  1:1015980/100‑1 (MQ=255)
                                                                                                |                                                                                                 
AAAATAGATAACAAAAAGATGGAACCTCGTTAATCATAAAACAATAAAATTAAATATTCTCGCAGTATATGGCAGTCTAAAGCATCAAAGATTTGATCAACATCTTTCATTTTAGACATCTCCTTGCAATGTAAAATATCATGTATCAACAACATCTGGTGCAAATCCATGAGTCGAACTCGACATTCATCTTA  >  NC_000913/2989790‑2989983

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