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
A4 F17 I0 R1 92 90.7 2214160 82.3% 1822253 222.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 4,296,268 T→C 21.0% intergenic (+474/+168) gltP → / ← yjcO glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,296,2680TC21.0% 51.9 / 5.9 34intergenic (+474/+168)gltP/yjcOglutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base T (15/8);  new base C (2/5);  total (18/16)
Fisher's exact test for biased strand distribution p-value = 1.90e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑A‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTC  >  NC_000913/4296040‑4296502
                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                
tACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCACCCCCTGATGCGACGCTTACCTCGTCTTATCAGCCCTACCTCAACCACGGGAAAACCCTGTTTTACCGTGATTTTTTAGTCCGGAAAAGCCGTTTACGCCGCA‑Tccc                                                                                                                                                                                                                                       >  2:542898/1‑238 (MQ=11)
tACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCA‑TCCg                                                                                                                                                                                                                                       >  1:957404/1‑239 (MQ=37)
     cgcATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTACCGTCATTTTTTAATTCGGGAAAGGCGTTTAACCCGCA‑Tcccaaacc                                                                                                                                                                                                                                  >  2:757112/1‑233 (MQ=11)
     cgcACCCGAACTCAACGCCTGATGCGACGCTTGCCGGGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCA‑TCCGACATc                                                                                                                                                                                                                                  <  1:763378/239‑1 (MQ=9)
           cGACATCAACGCCCGGTGCTACGCTTGACCCGTTTTATCAGGCCTACGCCAGACAGCGCAATTGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGGCATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCA‑TCCGACATCAATGcc                                                                                                                                                                                                                            <  1:580900/239‑1 (MQ=11)
                          aTGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTATGTCGGATAAGGCGTTTCTGCCGCATCCGCCATCAACGCCTGATGCGTGTCTTAAGGAGTATTATACGGCCTACGCCCGACAGCGCAATAGCCTAGTTAAGCGTGATTTGGCAGTGCGGTAAAGACGTTTATG‑CGCACACCGCCATCACCGCATGAGGCGACCCTTaa                                                                                                                                                                                                             >  2:580900/1‑239 (MQ=2)
                                                                                                                                     cGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTaa                                                                                                                                                                                                             <  2:694593/132‑1 (MQ=33)
                                                                                                                                                                          cGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTgg                                                          >  1:1087371/1‑239 (MQ=17)
                                                                                                                                                                                    cgcAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCTCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTc                                                >  1:500581/1‑239 (MQ=255)
                                                                                                                                                                                    cgcAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTTTCAGGCCTATCTTAACCGTTGGTTAATTTTTc                                                >  1:572998/1‑239 (MQ=255)
                                                                                                                                                                                    cgcAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTCTCTTAACCGTTGGTTAATTTTTc                                                >  1:446483/1‑239 (MQ=255)
                                                                                                                                                                                    cgcAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTc                                                >  1:987047/1‑239 (MQ=255)
                                                                                                                                                                                    cgcAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑AACAGCGCACTAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCCCATCCGCCATCCATGTCTACATCGACGGTTGCCGGGTCTAATCAGGCCTATCTTAACGGTGGGTAAATTTTTc                                                >  2:471715/1‑239 (MQ=11)
                                                                                                                                                                                       aaTAGCCTGTTTTAGCGTGATTTTGGAGGTCGGATAAGGCGTTTAGGCCGCA‑ACCGACATCAACGGCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCaaa                                             <  1:649193/239‑1 (MQ=14)
                                                                                                                                                                                        aTAGGCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCaaa                                             <  1:946143/238‑1 (MQ=255)
                                                                                                                                                                                              tGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GCCAGCGCACTAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTCCG‑‑CCGCTTCCGCCATCACTGTCTGATGCGACGCTACCAGCGTCTTTTCCGGCCTATCTTAACCCTTGGTTAATTTTTAAAAC‑CTTca                                      >  2:75987/1‑238 (MQ=11)
                                                                                                                                                                                              tGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTATGTCGGATAAGGCGTTT‑‑ACCCCACATCCGACATCAATGCCTGTTGCGCCGCTTGCCGCGCCTTTTCAGGCCCATTTTAACCGTTGGTTAATTTTTACAACCCTTc                                       >  2:712812/1‑238 (MQ=11)
                                                                                                                                                                                              tGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGATCGGATAAGGCGTTT‑‑ATGCCCCATCCGACATCAAGGCCTGATGCGACGCTTGCCGAGTCTTTTCAGGCCTACCTTCCCCGTTGGTGAATTTTTCaaaacctcca                                      >  2:242368/1‑232 (MQ=11)
                                                                                                                                                                                              cgttttAGGGTGTTTTTGTGGGTGGGATAGGGGCTTTATGGCGCA‑CCCGTGATCAACGCCGGAGGCGACGCTTAACGCGTCTTTACAGGCCTGCGCCA‑GACAGCGCAATTGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTca                                      <  2:210846/236‑1 (MQ=14)
                                                                                                                                                                                               gATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTcac                                     >  1:522758/1‑239 (MQ=255)
                                                                                                                                                                                                  ttaggggaaTTTTGGAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACAcc                                  <  1:757112/231‑1 (MQ=255)
                                                                                                                                                                                                  ttAGGGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACAcc                                  <  1:292606/239‑1 (MQ=255)
                                                                                                                                                                                                  tcaGCGTGATTTTGTAGGTCGGATAAGGCGTTTACGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTACCGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATCTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACAcc                                  <  1:223243/237‑1 (MQ=255)
                                                                                                                                                                                                   gagggggATTTTGGAGGTAGGAAAAGGCGTTTATGCCCGA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACAccc                                 <  1:800860/233‑1 (MQ=14)
                                                                                                                                                                                                   atgaatgtttttttTGGTCGGATAAGGGTTTTACGCCGCA‑CCCGCACTCAACGCGTAATGCGGCGCTGAACGGTTCTTTTCGGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCTTCCGATATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCCCAccc                                 <  2:657394/231‑1 (MQ=14)
                                                                                                                                                                                                          aTTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCa                          >  1:335884/1‑239 (MQ=255)
                                                                                                                                                                                                            tttGTAGGTTGGGTAAGGCTGTTAAGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCaaa                        <  1:356718/239‑1 (MQ=17)
                                                                                                                                                                                                            ttgtgaGGGCGGATAAGGCTTTTAAGCCGCA‑TCCGACATCAACGCCTTGTGCGACGCTTAACGCGTCTTATCAGGCCTGCGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGGCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCaaa                        <  1:75987/234‑1 (MQ=17)
                                                                                                                                                                                                                     cGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGTTTCGACGCTTGCCGCGCCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCCAACTCTTCAAACCCGGAATCAAAc                       >  1:657394/1‑231 (MQ=14)
                                                                                                                                                                                                                       gATAAGGCGTTTATGCCGAA‑TCCGACAACAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATa              <  1:471715/238‑1 (MQ=255)
                                                                                                                                                                                                                           agtcGTTTACGCCTCA‑TCCGACAACCACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCt         <  1:342142/236‑1 (MQ=17)
                                                                                                                                                                                                                           aGGCGTTTGTGCCGCA‑ACCGATATCAACGGCGTATGGAACGCTTCACGGGGCTTAGCAGGCCTACGGCATGAC‑GCGCAATAGTCAGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCTAAATCAAGGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACAGCCGGTATCAAACCCTTCCATACAGCt         <  2:1072896/239‑1 (MQ=17)
                                                                                                                                                                                                                                tttATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATACGACGCTTGCCGCGTCTGATCATGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAgg     >  1:1072896/1‑238 (MQ=255)
                                                                                                                                                                                                                                  tATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑ACGCCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTc  >  1:646359/1‑239 (MQ=255)
                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                
TACGCCGCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCATCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTTATGCCGCA‑TCCGACATCAACGCCTGATGCGACGCTTAACGCGTCTTATCAGGCCTACGCCA‑GACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGTTT‑‑A‑‑CCGCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTC  >  NC_000913/4296040‑4296502

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A