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
A1 F1 I1 R1 773 79.9 4112934 92.2% 3792125 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,297,077 C→T A17T (GCC→ACC)  yjcO ← Sel1 family TPR‑like repeat protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,297,0770CT100.0% 188.4 / NA 58A17T (GCC→ACC) yjcOSel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (28/30);  total (28/30)

CAATATTCGGCTTTGCTCAAATCGCCGGAGCTAAACCAGCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGCGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGAGTAACCAGTATAAAGAGTTCGAATGGATAAAAAAACAGCCTCCGAAAGGAGGC  >  NC_000913/4296956‑4297202
                                                                                                                         |                                                                                                                             
cAATATTCGGCTTTGCTCAAATCGCCGGAGCTAAACCAGCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCa                                                                                                              <  1:1826997/139‑1 (MQ=255)
   tatTCGGCTTTGCTCAAATCGCCGGAGCTAAACCAGCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCaaaa                                                                                                           >  2:654615/1‑139 (MQ=255)
    atTCGGCTTTGCTCAAATCGCCGGAGCTAAACCAGCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCaaaaa                                                                                                          <  1:449227/139‑1 (MQ=255)
             tGCTCAAATCGCCGGAGCTAAACCAGCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGaa                                                                                                                   >  1:2044643/1‑121 (MQ=255)
             tGCTCAAATCGCCGGAGCTAAACCAGCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGaa                                                                                                                   <  2:2044643/121‑1 (MQ=255)
             tGCTCAAATCGCCGGAGCTAAACCAGCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCaa                                                                                                 >  2:805217/1‑139 (MQ=255)
                        ccGGAGCTAAACCAGCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCaaa                                                                                                            <  1:1287843/117‑1 (MQ=255)
                        ccGGAGCTAAACCAGCTCTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCaaa                                                                                                            >  2:1287843/1‑117 (MQ=255)
                         cGGAGCTAAACCAGCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGa                                                                                                                    <  2:1588978/108‑1 (MQ=255)
                         cGGAGCTAAACCAGCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGa                                                                                                                    >  1:1588978/1‑108 (MQ=255)
                         cGGAGCTAAACCAGCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAAtttt                                                                                     >  2:105021/1‑139 (MQ=255)
                                      gCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGata                                                                        >  2:216054/1‑139 (MQ=255)
                                       cTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCGCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGataa                                                                       <  2:1435153/139‑1 (MQ=255)
                                         gTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGataata                                                                     <  2:754236/139‑1 (MQ=255)
                                             gCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGAt                                                                 <  1:105021/139‑1 (MQ=255)
                                                           tgCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGa                                                       >  2:1280390/1‑135 (MQ=255)
                                                           tgCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGa                                                       <  1:1280390/135‑1 (MQ=255)
                                                           tgCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGAGTaa                                                   <  1:654615/139‑1 (MQ=255)
                                                            gcgcGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGa                                                                                            >  1:1716789/1‑97 (MQ=255)
                                                            gcgcGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGa                                                                                            <  2:1716789/97‑1 (MQ=255)
                                                             cgcgTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAaac                                                                                                         >  2:1993981/1‑83 (MQ=255)
                                                             cgcgTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAaac                                                                                                         <  1:1993981/83‑1 (MQ=255)
                                                              gcgTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGAGTAACCa                                                >  2:184776/1‑139 (MQ=255)
                                                               cgTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGataa                                                                       >  1:1941241/1‑115 (MQ=255)
                                                               cgTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGataa                                                                       <  2:1941241/115‑1 (MQ=255)
                                                                gTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCaaa                                                                                                            >  2:699031/1‑77 (MQ=255)
                                                                gTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCaaa                                                                                                            <  1:699031/77‑1 (MQ=255)
                                                                gTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCAtt                                                                              >  2:1559774/1‑107 (MQ=255)
                                                                gTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCAtt                                                                              <  1:1559774/107‑1 (MQ=255)
                                                                     tCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCAt                                                                               >  1:156760/1‑101 (MQ=255)
                                                                     tCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCAt                                                                               <  2:156760/101‑1 (MQ=255)
                                                                     tCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGataa                                                                       >  2:1321534/1‑109 (MQ=255)
                                                                     tCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGataa                                                                       <  1:1321534/109‑1 (MQ=255)
                                                                     tCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGAGTAACCAGTATaaa                                         >  2:1688230/1‑139 (MQ=255)
                                                                          ggCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCAtttt                                                                            <  2:1849615/99‑1 (MQ=255)
                                                                          ggCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCAtttt                                                                            >  1:1849615/1‑99 (MQ=255)
                                                                          ggCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGAGTAACCAGTATAAAGAGtt                                    >  1:943157/1‑139 (MQ=255)
                                                                             ctctGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGAGTAACCAGTATAAAGAGTTCGa                                 <  2:943157/139‑1 (MQ=255)
                                                                                tgctgcCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCa                                                                                <  2:1053266/89‑1 (MQ=255)
                                                                                tgctgcCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCa                                                                                >  1:1053266/1‑89 (MQ=255)
                                                                                tgctgcCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGAGTAACCAGTATAAAGAGTTCGAATg                              >  1:1387143/1‑139 (MQ=255)
                                                                                     ccTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCAtttt                                                                            >  2:1706064/1‑88 (MQ=255)
                                                                                     ccTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCAtttt                                                                            <  1:1706064/88‑1 (MQ=255)
                                                                                      cTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGataa                                                                       <  2:150921/92‑1 (MQ=255)
                                                                                      cTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGataa                                                                       >  1:150921/1‑92 (MQ=255)
                                                                                              aCTGGCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGAGTAACCAGTATAAAGAGTTCGAATGGATAAAAAAACAGc                <  1:1688230/139‑1 (MQ=255)
                                                                                                 ggCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGa                                                                                                                    >  2:1278150/1‑36 (MQ=255)
                                                                                                 ggCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGa                                                                                                                    <  1:1278150/36‑1 (MQ=255)
                                                                                                 ggCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCa                                                                                                              <  1:1991827/42‑1 (MQ=255)
                                                                                                 ggCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCa                                                                                                              >  2:1991827/1‑42 (MQ=255)
                                                                                                 ggCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGataa                                                                       >  2:113195/1‑81 (MQ=255)
                                                                                                 ggCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGataa                                                                       <  1:113195/81‑1 (MQ=255)
                                                                                                  gCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAATCAACATCAATGCGATAATTTTTTTCATTTTGataa                                                                       >  1:1456116/1‑80 (MQ=255)
                                                                                                  gCTGCCAGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGataa                                                                       <  2:1456116/80‑1 (MQ=255)
                                                                                                        aGGCTCGGAGTCGTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGAGTAACCAGTATAAAGAGTTCGAATGGATAAAAAAACAGCCTCCGAAagg      <  2:255041/139‑1 (MQ=255)
                                                                                                            tCGGAGTCGTTGGTGTGGGGAAAGAATGTCAAAAACAACATCAATGCGAGAATGTTTTTCATCTTTATAATACGAATGGGTAGGGAGTAATCAGTATAAAGAGTTCGAAAGAATAAAAAAACAGCCACCGAAAGGAGGc  <  1:575836/139‑1 (MQ=255)
                                                                                                                    gTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGAGTAACCAGTATAAAGAGTTCGaa                                <  1:1510535/101‑1 (MQ=255)
                                                                                                                    gTTGGTGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGAGTAACCAGTATAAAGAGTTCGaa                                >  2:1510535/1‑101 (MQ=255)
                                                                                                                         |                                                                                                                             
CAATATTCGGCTTTGCTCAAATCGCCGGAGCTAAACCAGCTGTCGGCAAGAAAATATTGTGCGCGTCGGTCCCCGGCCTCTGCTGCCTTTAAATACTGGCTGCCAGGCTCGGAGTCGTTGGCGTGGGCAAAGAATGTCAAAAACAACATCAATGCGATAATTTTTTTCATTTTGATAATACGATTGGGTAGGGAGTAACCAGTATAAAGAGTTCGAATGGATAAAAAAACAGCCTCCGAAAGGAGGC  >  NC_000913/4296956‑4297202

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ 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