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
A11 F1 I1 R1 757 76.1 3598070 93.4% 3360597 108.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,796,296 C→T T208M (ACG→ATG)  csiR → transcriptional repressor of csiD

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,796,2960CT100.0% 198.1 / NA 61T208M (ACG→ATG) csiRtranscriptional repressor of csiD
Reads supporting (aligned to +/- strand):  ref base C (0/0);  new base T (27/34);  total (27/34)

ATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAACTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGATTTTA  >  NC_000913/2796163‑2796421
                                                                                                                                     |                                                                                                                             
aTCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCaa                                                                                                                          >  2:46641/1‑139 (MQ=255)
 tCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCACCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGCGAGTTAATGCGCCAGCAGTTACTGATGCCAAt                                                                                                                         <  1:380725/139‑1 (MQ=255)
       tGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCAt                                                                                                                   >  2:1007321/1‑139 (MQ=255)
         cggcgAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTa                                                                                                                 >  2:482419/1‑139 (MQ=255)
              aaCGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCcag                                                                                                            <  1:1007321/139‑1 (MQ=255)
              aaCGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCcag                                                                                                            <  1:1243963/139‑1 (MQ=255)
                  gTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAgg                                                                                                        <  1:482419/139‑1 (MQ=255)
                   tGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGc                                                                                                       >  2:1010245/1‑139 (MQ=255)
                   tGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGc                                                                                                       >  2:749744/1‑139 (MQ=255)
                           gTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTa                                                                                                                 <  2:844024/121‑1 (MQ=255)
                           gTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTa                                                                                                                 >  1:844024/1‑121 (MQ=255)
                              gAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCa                                                                                            <  2:282669/139‑1 (MQ=255)
                                aaTGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGAtggctgg                                                                                              >  1:1381190/1‑135 (MQ=255)
                                aaTGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGAtggctgg                                                                                              <  2:1381190/135‑1 (MQ=255)
                                      ggaggaTAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAattaatta                                                                                    <  2:561071/139‑1 (MQ=255)
                                      ggaggaTAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAattaatta                                                                                    >  1:898336/1‑139 (MQ=255)
                                        aggaTAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAattact                                                                                  <  1:749744/139‑1 (MQ=255)
                                        aggaTAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAattact                                                                                  <  1:1010245/139‑1 (MQ=255)
                                          gaTAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTActct                                                                                >  2:1549939/1‑139 (MQ=255)
                                              aaCACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCg                                                                            <  1:1720008/139‑1 (MQ=255)
                                              aaCACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCg                                                                            <  2:1495006/139‑1 (MQ=255)
                                                       aGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCa                                                                   >  1:515762/1‑139 (MQ=255)
                                                       aGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCa                                                                   <  2:1690598/139‑1 (MQ=255)
                                                              gACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGa                                                                          >  1:831850/1‑125 (MQ=255)
                                                              gACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGa                                                                          <  2:831850/125‑1 (MQ=255)
                                                                cccTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATCATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGcc                                                          <  1:46641/139‑1 (MQ=255)
                                                                   tGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGc                                                           >  1:1553048/1‑135 (MQ=255)
                                                                   tGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGc                                                           <  2:1553048/135‑1 (MQ=255)
                                                                    gACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCgg                                                      >  2:145152/1‑139 (MQ=255)
                                                                         cggcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAAt                                                                                                                         >  1:1784343/1‑67 (MQ=255)
                                                                         cggcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAAt                                                                                                                         <  2:1784343/67‑1 (MQ=255)
                                                                         cggcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGAtggctgg                                                                                              <  2:752040/94‑1 (MQ=255)
                                                                         cggcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGAtggctgg                                                                                              >  1:752040/1‑94 (MQ=255)
                                                                         cggcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGc                                                                    <  1:1793294/120‑1 (MQ=255)
                                                                         cggcggTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGc                                                                    >  2:1793294/1‑120 (MQ=255)
                                                                                    gcgcGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGACTACGCAACGCTTGCCCCGGATAAATTTTATCCggg                                      <  1:954292/139‑1 (MQ=255)
                                                                                              ccGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCa                            <  2:898336/139‑1 (MQ=255)
                                                                                              ccGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCa                            <  1:715543/139‑1 (MQ=255)
                                                                                              ccGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCa                            <  1:236203/139‑1 (MQ=255)
                                                                                                gcgcgcgcCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATc                          <  2:318129/139‑1 (MQ=255)
                                                                                                   cgcgcCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGAt                                                    <  2:1087940/110‑1 (MQ=255)
                                                                                                   cgcgcCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGAt                                                    >  1:1087940/1‑110 (MQ=255)
                                                                                                   cgcgcCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGt                       >  1:93571/1‑139 (MQ=255)
                                                                                                    gcgcCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGtt                      >  2:343179/1‑139 (MQ=255)
                                                                                                     cgcCAGTGAGTTAATGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGttt                     >  1:1238915/1‑139 (MQ=255)
                                                                                                                 aaTGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCa                                                                                            >  2:1422788/1‑56 (MQ=255)
                                                                                                                 aaTGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCa                                                                                            <  1:1422788/56‑1 (MQ=255)
                                                                                                                   tGCGCCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGa       <  2:515762/139‑1 (MQ=255)
                                                                                                                     cgcCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGa                                                     >  2:1474219/1‑91 (MQ=255)
                                                                                                                     cgcCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGa                                                     <  1:1474219/91‑1 (MQ=255)
                                                                                                                     cgcCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTAtt                  <  2:977537/126‑1 (MQ=255)
                                                                                                                     cgcCAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTAtt                  >  1:977537/1‑126 (MQ=255)
                                                                                                                       ccAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGAtttt   >  2:300289/1‑139 (MQ=255)
                                                                                                                       ccAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGAtttt   >  2:660931/1‑139 (MQ=255)
                                                                                                                        cAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCa                            >  2:596050/1‑113 (MQ=255)
                                                                                                                        cAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCa                            <  1:596050/113‑1 (MQ=255)
                                                                                                                        cAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGATTTTa  <  2:1238915/139‑1 (MQ=255)
                                                                                                                        cAGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGATTTTa  <  1:300289/139‑1 (MQ=255)
                                                                                                                        cAGCATTTACTGATGCCAATTCCCAATATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTCATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGATTTTa  <  1:660931/139‑1 (MQ=255)
                                                                                                                         aGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGa                                                     >  2:408081/1‑87 (MQ=255)
                                                                                                                         aGCATTTACTGATGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAATTACTCTTCCGGAATACGCAACACTTGCCCCGGa                                                     <  1:408081/87‑1 (MQ=255)
                                                                                                                                     |                                                                                                                             
ATCTGGCTGCGGCGAACGGTGCTTTCGGTGGAAATGCTGGAGGATAAACACGATCAGCACCAGACCCTGACTGCGGCGGTACTGGCGCGAGATACCGCGCGCGCCAGTGAGTTAATGCGCCAGCATTTACTGACGCCAATTCCCATTATCCAGCAGGCGATGGCTGGCAATTAACTACTCTTCCGGAATACGCAACACTTGCCCCGGATAAATTTTATCCGGGCTTTTTAGCATCGGTTTATTCGCTTCGAAGATTTTA  >  NC_000913/2796163‑2796421

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A