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
A31 F60 I1 R1 12 72.5 2467260 98.8% 2437652 139.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 1,593,525 A→C pseudogene (4562/5422 nt) yneO ← AIDA‑I family autotransporter YneO

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,593,5250AC98.2% 207.3 / ‑3.3 56pseudogene (4562/5422 nt)yneOAIDA‑I family autotransporter YneO
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base C (31/24);  minor base . (0/1);  total (31/25)
Fisher's exact test for biased strand distribution p-value = 4.46e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.24e-01

CTGCGCGTTGCTACTCCACTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGACCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGATGGGCCTTCC  >  NC_000913/1593388‑1593661
                                                                                                                                         |                                                                                                                                        
cTGCGCGTTGCTACTCCACTGCGCCAAATCGCCGCCTAGCTGCAGTACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGccc                                                                                                                                        <  1:1126052/140‑1 (MQ=255)
        tGCTACTCCACTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGaa                                                                                                                                >  1:1068541/1‑140 (MQ=255)
        tGCTACTCCACTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGaa                                                                                                                                >  2:539919/1‑140 (MQ=255)
        ctccaCTCCACTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGaa                                                                                                                                <  1:530962/136‑1 (MQ=255)
            aCTCCACTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCa                                                                                                                            <  1:50424/140‑1 (MQ=255)
               ccACTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTg                                                                                                                         <  1:960599/140‑1 (MQ=255)
               ccACTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTg                                                                                                                         <  1:17800/140‑1 (MQ=255)
               ccACTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTg                                                                                                                         <  1:407607/140‑1 (MQ=255)
                  cTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAAt                                                                                                                      <  1:291473/140‑1 (MQ=255)
                  cTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAAt                                                                                                                      <  1:632011/140‑1 (MQ=255)
                  cTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAAt                                                                                                                      >  2:646853/1‑140 (MQ=255)
                  cTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAAt                                                                                                                      >  1:1137381/1‑140 (MQ=255)
                     cgcCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTg                                                                                                                   >  1:865764/1‑140 (MQ=255)
                        cAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGCCATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGtat                                                                                                                >  1:839266/1‑140 (MQ=255)
                           aTCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACt                                                                                                             <  2:405835/140‑1 (MQ=255)
                               ccgccTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCgg                                                                                                         <  1:245921/140‑1 (MQ=255)
                                        tGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCG‑CCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGa                                                                                               <  2:976624/140‑1 (MQ=255)
                                            aTACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACgg                                                                                            <  2:882156/140‑1 (MQ=255)
                                            aTACATAGCGATTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACATTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACgg                                                                                            <  1:12816/140‑1 (MQ=255)
                                             tACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGt                                                                                           <  1:619035/140‑1 (MQ=255)
                                                aTAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCgt                                                                                        >  1:311450/1‑140 (MQ=255)
                                                  aGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCgtgc                                                                                      >  2:135373/1‑139 (MQ=255)
                                                      gTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAAc                                                                                  <  1:210177/140‑1 (MQ=255)
                                                      gTTAGCCTGAGTAGTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAAc                                                                                  <  2:867221/140‑1 (MQ=255)
                                                         aGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGAt                                                                               >  1:1117491/1‑140 (MQ=255)
                                                           ccTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATgg                                                                             <  1:646853/140‑1 (MQ=255)
                                                                gTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTaaa                                                                        >  1:937828/1‑140 (MQ=255)
                                                                 tATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAAc                                                                       <  2:865764/140‑1 (MQ=255)
                                                                    ttAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGc                                                                    >  2:819311/1‑140 (MQ=255)
                                                                           aCCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTgg                                                             >  1:690493/1‑140 (MQ=255)
                                                                           aCCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTgg                                                             >  1:840329/1‑140 (MQ=255)
                                                                           aCCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTgg                                                             >  2:4193/1‑140 (MQ=255)
                                                                               tCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGc                                                         <  1:459098/140‑1 (MQ=255)
                                                                                 aCCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCgg                                                       <  2:311450/140‑1 (MQ=255)
                                                                                       ccTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGt                                                 <  2:968511/140‑1 (MQ=255)
                                                                                         ttGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTg                                               >  2:300817/1‑140 (MQ=255)
                                                                                               gTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGata                                         >  2:820612/1‑140 (MQ=255)
                                                                                               gTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGata                                         >  2:202664/1‑140 (MQ=255)
                                                                                                   gTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGc                                     >  1:307176/1‑140 (MQ=255)
                                                                                                      cccTCCGACATGAGGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTc                                  >  1:648811/1‑140 (MQ=255)
                                                                                                       ccTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTcc                                 <  1:819311/140‑1 (MQ=255)
                                                                                                        cTCCGACATGACGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCg                                >  2:798807/1‑140 (MQ=255)
                                                                                                               aTGAGGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCg                         <  2:648811/140‑1 (MQ=255)
                                                                                                                  aCGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATTCTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGc                      <  1:303291/140‑1 (MQ=255)
                                                                                                                   cGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCg                     >  1:487126/1‑140 (MQ=255)
                                                                                                                   cGCATCCACATACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCg                     >  1:160518/1‑140 (MQ=255)
                                                                                                                            aTACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGa            >  1:706908/1‑140 (MQ=255)
                                                                                                                            aTACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGa            >  1:183780/1‑140 (MQ=255)
                                                                                                                             tACTGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGAt           <  1:637374/140‑1 (MQ=255)
                                                                                                                                tGCTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGATggg        >  1:1161327/1‑140 (MQ=255)
                                                                                                                                  cTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGATGGGcc      >  2:808087/1‑140 (MQ=255)
                                                                                                                                  cTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGATGGGcc      >  2:97474/1‑140 (MQ=255)
                                                                                                                                  cTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGATGGGcc      >  1:853218/1‑140 (MQ=255)
                                                                                                                                  cTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGATGGGcc      >  1:445125/1‑140 (MQ=255)
                                                                                                                                  cTTGCCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGATGGGcc      >  2:1158823/1‑140 (MQ=255)
                                                                                                                                  cTTACCGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGATGGGcc      >  1:23022/1‑140 (MQ=255)
                                                                                                                                      ccGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGATGGGCCTTcc  <  2:1068541/140‑1 (MQ=255)
                                                                                                                                      ccGCCCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGATGGGCCTTcc  <  2:109048/140‑1 (MQ=255)
                                                                                                                                         |                                                                                                                                        
CTGCGCGTTGCTACTCCACTGCGCCAAATCGCCGCCTAGCTGCAATACATAGCGGTTAGCCTGAGTATTTAGCTGACCGTCACCGGCCCTTGAACGTTCGTGCCCTCCGACATGACGCATCCACATACTGCTTGCCGACCCCTGAGAATGCAGTGAATCTGTATACTGCGGCTCACCCAGACGGTCGTGTAAACGATGGCTAAACAGCGAGTTGGCTGCGGCAATGTTGCTGATATAGCTTCCGGCCTCCGGGCGATAAACTGATGGGCCTTCC  >  NC_000913/1593388‑1593661

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A