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
A22 F44 I0 R1 387 90.4 3244086 98.5% 3195424 139.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 1,113,548 T→C 7.3% intergenic (+142/‑31) opgH → / → yceK OPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist/outer membrane integrity lipoprotein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009131,113,5480TC 7.3% 169.6 / 3.8 55intergenic (+142/‑31)opgH/yceKOPG biosynthetic ACP‑dependent transmembrane UDP‑glucose beta‑1,2 glycosyltransferase; nutrient‑dependent cell size regulator, FtsZ assembly antagonist/outer membrane integrity lipoprotein
Reads supporting (aligned to +/- strand):  ref base T (28/23);  new base C (2/2);  total (30/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.31e-01

AATAAAAACGTAGTTGCCTGATGCGCTACGCTTATCAGGCCTACATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCGGGGCAGGGGCATGGCAACCAATATTATCC  >  NC_000913/1113402‑1113682
                                                                                                                                                  |                                                                                                                                       
aaTAAAAACGTAGTTGCCTGATGCGCTACGCTTATCAGGCCTACATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGc                                                                                                                                       >  4:563958/1‑149 (MQ=255)
   aaaaaCGTAGTTGCCTGATGCGCTACGCTTATCAGGCCTACATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCgg                                                                                                                                    >  4:47402/1‑149 (MQ=255)
               gCCTGATGCGCTACGCTTATCAGGCCTACATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑Attttt                                                                                                                            <  1:504119/144‑1 (MQ=255)
               gCCTGATGCGCTACGCTTATCAGGCCTACATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑Attttt                                                                                                                            >  2:504119/1‑144 (MQ=255)
                     tGCGCTACGCTTATCAGGCCTACATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAagag                                                                                                                 <  3:281499/149‑1 (MQ=255)
                        gcTACGCTTATCAGGCCTACATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTa                                                                                                              >  2:712280/1‑149 (MQ=255)
                             gCTTATCAGGCCTACATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCAAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAagag                                                                                                                 <  3:122075/141‑1 (MQ=255)
                             gCTTATCAGGCCTACATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCAAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAagag                                                                                                                 >  4:122075/1‑141 (MQ=255)
                                   cAGGCCTACATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGtt                                                                                                   <  3:563958/149‑1 (MQ=255)
                                      gCCTACATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTaa                                                                                                >  3:428501/1‑149 (MQ=255)
                                          aCATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGc                                                                                                                                       >  2:361958/1‑107 (MQ=255)
                                          aCATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGc                                                                                                                                       <  1:361958/107‑1 (MQ=255)
                                            aTCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGt                                                                                                    <  3:786503/139‑1 (MQ=255)
                                            aTCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGt                                                                                                    >  4:786503/1‑139 (MQ=255)
                                            aTCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTgtgg                                                                                          <  1:712280/149‑1 (MQ=255)
                                            aTCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTgtgg                                                                                          >  3:167724/1‑149 (MQ=255)
                                                ttCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAg                                                                                      >  1:359726/1‑149 (MQ=255)
                                                ttCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAg                                                                                      >  3:279450/1‑149 (MQ=255)
                                                   cTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCATAACGCCGGT‑At                                                                                                                                <  1:518405/104‑1 (MQ=255)
                                                   cTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCATAACGCCGGT‑At                                                                                                                                >  2:518405/1‑104 (MQ=255)
                                                        aTTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATgg                                                                              >  3:559918/1‑149 (MQ=255)
                                                            aTTGATTTTGCAAGGCTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTCTGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGAc                                                                          >  3:58739/1‑149 (MQ=255)
                                                            aTTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGAc                                                                          >  1:612724/1‑149 (MQ=255)
                                                                aTTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTg                                                                      >  3:615749/1‑149 (MQ=255)
                                                                aTTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTg                                                                      >  3:430607/1‑149 (MQ=255)
                                                                 ttttGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGc                                                                     <  4:615749/149‑1 (MQ=255)
                                                                     gCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAg                                                                 <  2:359726/149‑1 (MQ=255)
                                                                      cAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGt                                                                <  3:47402/149‑1 (MQ=255)
                                                                       aaGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTg                                                               >  4:517540/1‑149 (MQ=255)
                                                                        aGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTgg                                                              >  3:131693/1‑149 (MQ=255)
                                                                                 gggTCGGATGAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCCTGGTGACCTTGCTGAGTGGCTGTGgcag                                                     >  4:689197/1‑149 (MQ=255)
                                                                                   gTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGgcagca                                                   <  1:260692/149‑1 (MQ=255)
                                                                                   gTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGgcagca                                                   >  2:643526/1‑149 (MQ=255)
                                                                                    tCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCat                                                  <  4:167724/149‑1 (MQ=255)
                                                                                      ggATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCatta                                                >  3:379157/1‑149 (MQ=255)
                                                                                           aGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGt                                           <  4:58739/149‑1 (MQ=255)
                                                                                               gTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCa                                       <  4:112122/149‑1 (MQ=255)
                                                                                                      ccgcATCAGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATAcc                                <  3:689197/149‑1 (MQ=255)
                                                                                                        gcATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCgg                              <  4:733749/149‑1 (MQ=255)
                                                                                                             cGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCggggcag                         <  4:559918/149‑1 (MQ=255)
                                                                                                             cGGAAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCggggcag                         <  3:517540/149‑1 (MQ=255)
                                                                                                              ggCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGACTGTGGCAGCATTATTAGTCGCACTATACCggggcagg                        >  2:408280/1‑149 (MQ=255)
                                                                                                               gCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCggggcaggg                       >  2:475374/1‑149 (MQ=255)
                                                                                                                cAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCggggcagggg                      <  4:428501/149‑1 (MQ=255)
                                                                                                                     acaacGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATGATTAGTCGCACTATACCGGGGCAGGGGCATgg                 >  4:654912/1‑149 (MQ=255)
                                                                                                                      caacGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGCGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCGGGGCAGGGGCATGGc                <  3:428488/149‑1 (MQ=255)
                                                                                                                          caaccAAAAAAAATAACGGGGTTATGGCGGTAATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCGGGGCAGGGGCATGGCAAc             <  4:641041/146‑1 (MQ=255)
                                                                                                                              ctaTAAAAATACCGGCGTTATGCCGGT‑ATTTTTTCACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCGGGGCAGGGGCATGGCAACCAata        <  3:654912/147‑1 (MQ=255)
                                                                                                                               aaTAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCGGGGCAGGGGCATGGCAACCAatat       >  2:609177/1‑149 (MQ=255)
                                                                                                                                aTAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCGGGGCAGGGGCATGGCAACCAAtatt      >  2:80974/1‑149 (MQ=255)
                                                                                                                                 tAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGa                                                                           >  4:184636/1‑79 (MQ=255)
                                                                                                                                 tAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGa                                                                           <  3:184636/79‑1 (MQ=255)
                                                                                                                                    aaaTACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCGGGGCAGGGGCATGGCAACCAATATTATcc  >  1:430768/1‑149 (MQ=255)
                                                                                                                                    aaaTACCGGCATAACGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCggggcaggggc                     >  1:753299/1‑130 (MQ=255)
                                                                                                                                    aaaTACCGGCATAACGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCggggcaggggc                     <  2:753299/130‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                       
AATAAAAACGTAGTTGCCTGATGCGCTACGCTTATCAGGCCTACATCGTTCCTGCAATTTATTGATTTTGCAAGACTTTGTGGGTCGGATAAGGCGTTCACGCCGCATCCGGCAAAAACAACGAGCCAATAAAAATACCGGCGTTATGCCGGT‑ATTTTTTTACGAAAGAGGTATCAAATGCGTTTAATTGTGGTGAGCATCATGGTGACCTTGCTGAGTGGCTGTGGCAGCATTATTAGTCGCACTATACCGGGGCAGGGGCATGGCAACCAATATTATCC  >  NC_000913/1113402‑1113682

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