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
A3 F1 I1 R1 57 49.8 2216334 94.8% 2101084 113.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,765,666 T→C T37T (ACA→ACG)  yfjM ← CP4‑57 prophage, uncharacterized protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,765,6660TC100.0% 241.2 / NA 64T37T (ACA→ACG) yfjMCP4‑57 prophage, uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (35/29);  total (35/29)

CATATCTCGATGCTCTTTGAGCAATGTCAACATCGCGTGTTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGA  >  NC_000913/2765534‑2765800
                                                                                                                                    |                                                                                                                                      
cATATCTCGATGCTCTTTGAGCAATGTCAACATCGCGTGTTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCg                                                                                                                                  <  1:324437/139‑1 (MQ=255)
  tatCTCGATGCTCTTTGAGCAATGTCAACATCGCGTGTTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGAc                                                                                                                                >  2:713623/1‑139 (MQ=255)
    tctcGATGCTCTTTGAGCAATGTCAACATCGCGTGTTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCGCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGt                                                                                                                              >  2:699777/1‑139 (MQ=255)
                    gCAATGTCAACATCGCGTGTTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTc                                                                                                              >  2:297639/1‑139 (MQ=255)
                      aaTGTCAACATCGCGTGTTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTctg                                                                                                            <  1:134951/139‑1 (MQ=255)
                       aTGTCAACATCGCGTGTTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTctgc                                                                                                           >  1:925206/1‑139 (MQ=255)
                        tGTCAACATCGCGTGTTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTctgct                                                                                                          >  1:598198/1‑139 (MQ=255)
                         gTCAACATCGCGTGTTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGTCGTAGAATTTTTTCTTGTctgctg                                                                                                         >  1:616350/1‑139 (MQ=255)
                              cATCGCGTGTTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGaa                                                                                                    <  2:39761/139‑1 (MQ=255)
                                   cgTGTTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAAtt                                                                                               >  2:594231/1‑139 (MQ=255)
                                    gtgtTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTa                                                                                              >  1:752993/1‑139 (MQ=255)
                                     tgtTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTAc                                                                                             <  2:280012/139‑1 (MQ=255)
                                          aTGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGt                                                                                        >  1:1002296/1‑139 (MQ=255)
                                                      atTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTtgctg                                                                            <  2:752993/139‑1 (MQ=255)
                                                          ttgATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTg                                                                        >  2:828330/1‑139 (MQ=255)
                                                            gATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGt                                                                      <  2:283517/139‑1 (MQ=255)
                                                            gATGCCTTGCCCATCCGGACCCCACCCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACATAGAATTTTTTCTTGTCTGCTGGTGAATAATTAATAAGTATCGAGTTGCTGCTTGGt                                                                      >  2:272606/1‑139 (MQ=255)
                                                             aTGCCTTGCCCATCCGGACCCCACTCCTTATCGCTCATCATTATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTg                                                                     >  2:314349/1‑139 (MQ=255)
                                                             aTGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTg                                                                     >  2:700053/1‑139 (MQ=255)
                                                             aTGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTg                                                                     >  2:582430/1‑139 (MQ=255)
                                                             aTGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTg                                                                     >  2:604032/1‑139 (MQ=255)
                                                                 cTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACTTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGAt                                                                 >  2:791037/1‑139 (MQ=255)
                                                                 cTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACATAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGAt                                                                 <  1:272606/139‑1 (MQ=255)
                                                                  ttGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATc                                                                >  1:1106589/1‑139 (MQ=255)
                                                                    gCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAg                                                              >  2:396239/1‑139 (MQ=255)
                                                                       cATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGaa                                                           <  2:925206/139‑1 (MQ=255)
                                                                                   aCTTCTTATAGCTCATCATGATGGCTTGTTGTGGGCTCTCTGCTCGTTCCGTTGTGACGTAGAATTTTTTCTTGGCTGCTGGAGAATAAGTACTTAGCATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGaa                                               <  2:504281/139‑1 (MQ=255)
                                                                                   aCTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGaa                                               >  1:247284/1‑139 (MQ=255)
                                                                                   aCTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCATTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGaa                                               <  1:699777/139‑1 (MQ=255)
                                                                                    cTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGaaa                                              >  1:941386/1‑139 (MQ=255)
                                                                                           taGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGa                                       <  1:603451/139‑1 (MQ=255)
                                                                                                 atcatGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACg                                                                                                                               <  1:247475/45‑1 (MQ=255)
                                                                                                 atcatGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACg                                                                                                                               >  2:247475/1‑45 (MQ=255)
                                                                                                 atcatGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACTTAGAATTTTTTCTTGTCTGCTGGCg                                                                                                      <  1:283771/70‑1 (MQ=255)
                                                                                                 atcatGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGt                                                                                                               >  1:183380/1‑61 (MQ=255)
                                                                                                 atcatGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGt                                                                                                               <  2:183380/61‑1 (MQ=255)
                                                                                                 atcatGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCg                                                                                                      >  2:283771/1‑70 (MQ=255)
                                                                                                 atcatGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGAcatcat                                 >  1:108450/1‑139 (MQ=255)
                                                                                                 atcatGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGAcatcat                                 <  2:941386/139‑1 (MQ=255)
                                                                                                 atcatGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGAcatcat                                 >  2:777325/1‑139 (MQ=255)
                                                                                                 atcatGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGAcatcat                                 <  1:713623/139‑1 (MQ=255)
                                                                                                 atcatGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGAcatcat                                 >  1:737518/1‑139 (MQ=255)
                                                                                                   catGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTAt                                                                                      <  1:597758/84‑1 (MQ=255)
                                                                                                   catGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTAt                                                                                      >  2:597758/1‑84 (MQ=255)
                                                                                                   catGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATcc                               >  2:729674/1‑139 (MQ=255)
                                                                                                   catGATGGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTGTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAgg                                                       <  1:658498/115‑1 (MQ=255)
                                                                                                   catGATGGCTTGTTTTGGGCTCTCTGCTCGTTACGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAgg                                                       >  2:658498/1‑115 (MQ=255)
                                                                                                    atgatgGCTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATccc                              <  2:1002296/139‑1 (MQ=255)
                                                                                                           cTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGt                                                                                                                              >  1:421140/1‑36 (MQ=255)
                                                                                                           cTTGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGt                                                                                                                              <  2:421140/36‑1 (MQ=255)
                                                                                                             tGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACt                                                                                            >  1:20901/1‑68 (MQ=255)
                                                                                                             tGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACt                                                                                            <  2:20901/68‑1 (MQ=255)
                                                                                                             tGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGACGAGGTTACCGAAACGAGGGAcatc                                   <  1:675456/125‑1 (MQ=255)
                                                                                                             tGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGAcatc                                   >  2:675456/1‑125 (MQ=255)
                                                                                                             tGTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTtgt                     >  2:1083510/1‑139 (MQ=255)
                                                                                                              gTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTtg                                                                               <  2:628031/80‑1 (MQ=255)
                                                                                                              gTTTTGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTtg                                                                               >  1:628031/1‑80 (MQ=255)
                                                                                                               ttttGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTgg                   <  1:396239/139‑1 (MQ=255)
                                                                                                                  tGGGCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACt                <  2:14944/139‑1 (MQ=255)
                                                                                                                    ggCTCTCTGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGc              >  2:539489/1‑139 (MQ=255)
                                                                                                                      ctctctGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGccc            <  2:993920/139‑1 (MQ=255)
                                                                                                                         tctGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGcccccc         <  1:729674/139‑1 (MQ=255)
                                                                                                                         tctGCTCGTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGcccccc         <  1:933278/139‑1 (MQ=255)
                                                                                                                                gTTCCGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGATATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGa  <  1:225726/139‑1 (MQ=255)
                                                                                                                                    |                                                                                                                                      
CATATCTCGATGCTCTTTGAGCAATGTCAACATCGCGTGTTCATGGCTTTCTATATTGTTGATGCCTTGCCCATCCGGACCCCACTCCTTATAGCTCATCATGATGGCTTGTTTTGGGCTCTCTGCTCGTTCTGTTTCGACGTAGAATTTTTTCTTGTCTGCTGGCGAATAATTACTAAGTATCGAGTTGCTGCTTGGTGAGATCAGGAAGAGGTTACCGAAACGATGGACATCATCCCCCATTTTGTGGACTGCCCCCCCGGTAGA  >  NC_000913/2765534‑2765800

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A