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 I2 R1 766 64.2 3232166 90.9% 2938038 104.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,169,693 C→T pseudogene (475/475 nt) gatR ← pseudogene, repressor for gat operon, interrupted by IS3, split galactitol utilization operon repressor, fragment 2, split galactitol utilization operon repressor, interrupted

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,169,6930CT100.0% 195.3 / NA 60pseudogene (475/475 nt)gatRpseudogene, repressor for gat operon, interrupted by IS3, split galactitol utilization operon repressor, fragment 2, split galactitol utilization operon repressor, interrupted
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (31/29);  total (31/29)

CCGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATACTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGG  >  NC_000913/2169561‑2169816
                                                                                                                                    |                                                                                                                           
ccGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACAcc                                                                                                                       >  2:1212406/1‑139 (MQ=255)
              ttgTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTAc                                                                                                         >  1:781726/1‑139 (MQ=255)
                 tCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGGTGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCcg                                                                                                      >  2:715004/1‑139 (MQ=255)
                     ttACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGtc                                                                                                  <  1:1212406/139‑1 (MQ=255)
                           ccaGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGc                                                                                            >  2:118530/1‑139 (MQ=255)
                              gATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTg                                                                                             <  1:1440373/135‑1 (MQ=255)
                              gATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTg                                                                                             >  2:1440373/1‑135 (MQ=255)
                                          ttGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                             <  1:1108126/139‑1 (MQ=255)
                                             cGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                             >  1:1571319/1‑136 (MQ=255)
                                             cGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                             <  2:1571319/136‑1 (MQ=255)
                                             cGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCAcc                                                                          >  1:599273/1‑139 (MQ=255)
                                                  aTCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACctc                                                                        >  2:1241388/1‑136 (MQ=255)
                                                  aTCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACctc                                                                        <  1:1241388/136‑1 (MQ=255)
                                                  aTCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGa                                                                     <  1:349212/139‑1 (MQ=255)
                                                       aCTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGac                                                                    <  1:1199676/135‑1 (MQ=255)
                                                       aCTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGac                                                                    >  2:1199676/1‑135 (MQ=255)
                                                            tctctcTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGcatca                                                           >  2:935190/1‑139 (MQ=255)
                                                                tctTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCgg                                                       >  1:116677/1‑139 (MQ=255)
                                                                 ctTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAAtatta                                                                                                                           >  1:725280/1‑70 (MQ=255)
                                                                 ctTGAACCAGGGAGAATCCGTAATGCCGAATGCGGTGTAAACACCTTATCCGGCATACAGAACAAtatta                                                                                                                           <  2:725280/70‑1 (MQ=255)
                                                                     aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTg                                                                                             <  2:580601/96‑1 (MQ=255)
                                                                     aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTg                                                                                             >  1:580601/1‑96 (MQ=255)
                                                                     aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGc                                                                                       >  2:1086797/1‑102 (MQ=255)
                                                                     aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGc                                                                                       <  1:1086797/102‑1 (MQ=255)
                                                                     aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCatcatc                                                         <  2:589502/132‑1 (MQ=255)
                                                                     aaCCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCatcatc                                                         >  1:589502/1‑132 (MQ=255)
                                                                          gggAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTaataataat                                             >  2:558327/1‑139 (MQ=255)
                                                                                aTCCGTAATGCCGGATGGGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAAt                                       >  2:1008393/1‑139 (MQ=255)
                                                                                    gTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGt                                                                                   <  2:1211062/91‑1 (MQ=255)
                                                                                    gTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGt                                                                                   >  1:1211062/1‑91 (MQ=255)
                                                                                    gTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAAttttt                                   >  1:1551864/1‑139 (MQ=255)
                                                                                      aaTGCCTGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                       <  2:956728/69‑1 (MQ=38)
                                                                                      aaTGCCGGATGCGGTGTAAACACCTTATCCGGAATACAGAACAATATTACACCGTAATTAATTTTAccc                                                                                                       >  1:956728/1‑69 (MQ=38)
                                                                                       aTGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCg                                >  1:1449578/1‑139 (MQ=255)
                                                                                        tGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACGCAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                               <  2:116677/139‑1 (MQ=255)
                                                                                        tGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                               <  1:558327/139‑1 (MQ=255)
                                                                                        tGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                               <  2:781726/139‑1 (MQ=255)
                                                                                           cGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACctc                                                                        <  1:1252702/95‑1 (MQ=255)
                                                                                           cGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACctc                                                                        >  2:1252702/1‑95 (MQ=255)
                                                                                             gATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGgt                          <  2:1449578/139‑1 (MQ=255)
                                                                                             gATGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTCATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGgt                          >  2:859393/1‑139 (MQ=255)
                                                                                              aTGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTaca                                                                                                                         >  2:926295/1‑43 (MQ=255)
                                                                                              aTGCGGTGTAAACACCTTATCCGGCATACAGAACAATATTaca                                                                                                                         <  1:926295/43‑1 (MQ=255)
                                                                                                  ggTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATc                                                                              <  2:284854/82‑1 (MQ=255)
                                                                                                  ggTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATc                                                                              >  1:284854/1‑82 (MQ=255)
                                                                                                  ggTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTAc                     <  1:715004/139‑1 (MQ=255)
                                                                                                  ggTGTAAACACCTTATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTAc                     <  1:859393/139‑1 (MQ=255)
                                                                                                              ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTAt                                                                               >  1:573802/1‑69 (MQ=255)
                                                                                                              ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTAt                                                                               <  2:573802/69‑1 (MQ=255)
                                                                                                              ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                             <  2:876353/71‑1 (MQ=255)
                                                                                                              ttATCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                             >  1:876353/1‑71 (MQ=255)
                                                                                                                aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTAt                                                                               >  2:283437/1‑67 (MQ=255)
                                                                                                                aTCCGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTAt                                                                               <  1:283437/67‑1 (MQ=255)
                                                                                                                  ccGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                             >  2:333390/1‑67 (MQ=255)
                                                                                                                  ccGGCATACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATcc                                                                             <  1:333390/67‑1 (MQ=255)
                                                                                                                     gCATACAGAAGAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACgg  <  1:1171248/139‑1 (MQ=255)
                                                                                                                       aTACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                               <  2:806492/108‑1 (MQ=255)
                                                                                                                       aTACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                               <  2:896045/108‑1 (MQ=255)
                                                                                                                       aTACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                               >  1:806492/1‑108 (MQ=255)
                                                                                                                       aTACAGAACAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                               >  1:896045/1‑108 (MQ=255)
                                                                                                                               cAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                               >  1:226004/1‑100 (MQ=255)
                                                                                                                               cAATATTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGa                               <  2:226004/100‑1 (MQ=255)
                                                                                                                                    |                                                                                                                           
CCGGCAGCGTTGCGTTGTCGATTACCACCAGATTGTCCACTGTTGCGTTAATCAAACTATTCTCTCTTGAACCAGGGAGAATCCGTAATGCCGGATGCGGTGTAAACACCTTATCCGGCATACAGAACAATACTACACCGTAATTAATTTTACCCGCGTCTTCTGCAATGCCAGTTTATCCACCTCTGACACAGCATCATCGGTAATAATAATGTCAATTTTTTCGATTGGTAGTACCTGATTAAAACCGCGACGG  >  NC_000913/2169561‑2169816

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A