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
A7 F1 I1 R1 776 60.0 3074904 90.1% 2770488 104.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,500,043 C→T pseudogene (492/942 nt) yjgX ← pseudogene fragment

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,500,0430CT100.0% 169.5 / NA 54pseudogene (492/942 nt)yjgXpseudogene fragment
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (27/27);  total (27/27)

TAAAGCATGGCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGCTAGGAGTTAAGGCTGTCACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCG  >  NC_000913/4499912‑4500178
                                                                                                                                   |                                                                                                                                       
tAAAGCATGGCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGt                                                                                                                                  <  1:1120492/139‑1 (MQ=255)
 aaaGCATGGCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGtt                                                                                                                                 <  1:120429/139‑1 (MQ=255)
 aaaGCATGGCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGtt                                                                                                                                 <  1:561563/139‑1 (MQ=255)
         gCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGt                                                                                                                         >  1:310361/1‑139 (MQ=255)
            aaaTGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGttac                                                                                                                      <  2:1142660/139‑4 (MQ=255)
             aaTGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTtaca                                                                                                                     <  2:690817/139‑1 (MQ=255)
             aaTGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTtaca                                                                                                                     <  2:578843/139‑1 (MQ=255)
                           cGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGGTGCTGGCGAGGTAACAGGTAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                                                       <  2:1334203/139‑1 (MQ=255)
                           cGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATg                                                                                                         >  1:778981/1‑137 (MQ=255)
                           cGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATg                                                                                                         <  2:778981/137‑1 (MQ=255)
                                aaGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTtac                                                                                                                      <  2:59102/119‑1 (MQ=255)
                                aaGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTtac                                                                                                                      >  1:59102/1‑119 (MQ=255)
                                   gATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCcatc                                                                                               <  2:825763/139‑1 (MQ=255)
                                             aGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGa                                                                                                           >  1:735969/1‑117 (MQ=255)
                                             aGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGa                                                                                                           <  2:735969/117‑1 (MQ=255)
                                               cTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGaaa                                                                                   >  2:598301/1‑139 (MQ=255)
                                                  gCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAAtt                                                                                <  1:593667/139‑1 (MQ=255)
                                                  gCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAAtt                                                                                >  2:711280/1‑139 (MQ=255)
                                                  gCCAAGAAACTTCTCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATAATTCGGGGATACTGCTCTAGGTAATTATTCTGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAATCTATCATGTGCAGGAAAAtt                                                                                >  2:994472/1‑139 (MQ=255)
                                                            ttATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCg                                                                         <  1:39777/136‑1 (MQ=255)
                                                            ttATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCg                                                                         >  2:39777/1‑136 (MQ=255)
                                                               tCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAgg                                                                   <  2:310361/139‑1 (MQ=255)
                                                                              cTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGAt                                                                                                          <  1:477119/85‑1 (MQ=255)
                                                                              cTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGAt                                                                                                          >  2:477119/1‑85 (MQ=255)
                                                                              cTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTCGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAgcg                                                    >  2:185801/1‑139 (MQ=255)
                                                                              cTGGCGAGGTAACAGGCAATTTTTCGAGGATATTGCTCCAGGTACTTATTCGGTTAGGAGGTAAGGCTGTTACACGGATTTGGAGGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAgcg                                                    >  2:913343/1‑139 (MQ=255)
                                                                                ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTacac                                                                                                                    <  1:1382913/73‑1 (MQ=255)
                                                                                ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTacac                                                                                                                    >  2:1382913/1‑73 (MQ=255)
                                                                                ggCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCa                                                  >  1:389114/1‑139 (MQ=255)
                                                                                      gTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGga                                                                       >  1:176358/1‑112 (MQ=255)
                                                                                      gTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGga                                                                       <  2:176358/112‑1 (MQ=255)
                                                                                      gTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAg                                                      >  1:405199/1‑129 (MQ=255)
                                                                                      gTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAg                                                      <  2:405199/129‑1 (MQ=255)
                                                                                      gTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCt                                            >  1:802294/1‑139 (MQ=255)
                                                                                                aTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGt                                               <  1:453484/126‑1 (MQ=255)
                                                                                                aTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGt                                               >  2:453484/1‑126 (MQ=255)
                                                                                                aTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTa                                  >  1:392938/1‑139 (MQ=255)
                                                                                                aTTTTTCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTa                                  <  1:711280/139‑1 (MQ=255)
                                                                                                 tttttCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGtt                                         >  2:1368357/1‑131 (MQ=255)
                                                                                                 tttttCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGtt                                         <  1:1368357/131‑1 (MQ=255)
                                                                                                     tCGGGGATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTaacaac                             <  2:389114/139‑1 (MQ=255)
                                                                                                         ggATACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGtt                         >  2:711206/1‑139 (MQ=255)
                                                                                                           aTACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGAt                                                                                                          >  2:463124/1‑56 (MQ=255)
                                                                                                           aTACTGCTCCAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGAt                                                                                                          <  1:463124/56‑1 (MQ=255)
                                                                                                                    cAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCAt                   <  1:879722/134‑1 (MQ=255)
                                                                                                                    cAGGTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCAt                   >  2:879722/1‑134 (MQ=255)
                                                                                                                      ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                                                       >  1:1460387/1‑48 (MQ=255)
                                                                                                                      ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATgag                                                                                                       <  2:1460387/48‑1 (MQ=255)
                                                                                                                      ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCGTGTGCAGGAAAATTATCtt                                                                           >  2:47775/1‑76 (MQ=255)
                                                                                                                      ggTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCGTGTGCAGGAAAATTATCtt                                                                           <  1:47775/76‑1 (MQ=255)
                                                                                                                       gTAATTATTCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTa           >  1:19856/1‑139 (MQ=255)
                                                                                                                           ttattCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCAc                                                 <  1:1359347/97‑1 (MQ=255)
                                                                                                                           ttattCGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCAc                                                 >  2:1359347/1‑97 (MQ=255)
                                                                                                                                cGGTTAGGAGTTAAGGCTGTTACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGgaagcg  >  1:1528264/1‑139 (MQ=255)
                                                                                                                                   |                                                                                                                                       
TAAAGCATGGCGAAATGACGTGAGTACCGGCGAAGGATACCATCAAGCTGGCCAAGAAAGTTATCCAGTTTACTGATGCTGGCGAGGTAACAGGCAATTTTTCGGGGATACTGCTCCAGGTAATTATTCGGCTAGGAGTTAAGGCTGTCACACGGATTTGGATGAGAACCCATCATGTGCAGGAAAATTATCTTCGGAGAGGATGTATCCGCCAGCGCACGTTCTGTTTCCTGTAACAACAGTTTGTCATCTGTTTTACGGGAAGCG  >  NC_000913/4499912‑4500178

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A