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
A5 F1 I1 R1 770 51.4 2439994 93.8% 2288714 110.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 986,671 A→G R104R (CGT→CGC)  ompF ← outer membrane porin 1a (Ia,b,F)

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913986,6710AG100.0% 220.8 / NA 61R104R (CGT→CGC) ompFouter membrane porin 1a (Ia,b,F)
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (31/30);  total (31/30)

GCTGTATGCAGTATCACCACCAAATTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGACGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGAATTGATTTGAGTTTCCCCTTTAAAACCAAGACGGGCA  >  NC_000913/986542‑986797
                                                                                                                                 |                                                                                                                              
gCTGTATGCAGTATCACCACCAAATTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTg                                                                                                                       <  2:785509/139‑1 (MQ=255)
    tATGCAGTATCACCACCAAATTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTAc                                                                                                                   <  2:302005/139‑1 (MQ=255)
            aTCACCACCAAATTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGa                                                                                                           <  2:83315/139‑1 (MQ=255)
              caccacCAAATTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGc                                                                                                         >  2:579750/1‑139 (MQ=255)
              caccacCAAATTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGc                                                                                                         >  2:470279/1‑139 (MQ=255)
                ccaccaAATTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGt                                                                                                       >  1:77360/1‑139 (MQ=255)
                 caccaAATTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTc                                                                                                      >  1:780546/1‑139 (MQ=255)
                  accaAATTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGt                                                                                                                           <  2:157355/117‑1 (MQ=255)
                  accaAATTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGt                                                                                                                           >  1:157355/1‑117 (MQ=255)
                     aaaTTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAgcg                                                                                                  >  2:511808/1‑139 (MQ=255)
                           tGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCa                                                                                            <  1:447056/139‑1 (MQ=255)
                             gcagcaTATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAg                                                                                                    >  1:867422/1‑129 (MQ=255)
                             gcagcaTATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAg                                                                                                    <  2:867422/129‑1 (MQ=255)
                                 caTATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAgttg                                                                                      >  2:176043/1‑139 (MQ=255)
                                         tgtAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTg                                                                              <  1:511808/139‑1 (MQ=255)
                                              cccAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGt                                                                         <  2:780546/139‑1 (MQ=255)
                                                   tGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGgcgc                                                                                                                             >  2:451611/1‑82 (MQ=255)
                                                   tGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGgcgc                                                                                                                             <  1:451611/82‑1 (MQ=255)
                                                   tGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAg                                                                                                    <  2:291236/107‑1 (MQ=255)
                                                   tGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAg                                                                                                    >  1:291236/1‑107 (MQ=255)
                                                   tGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCTTGGAAGTTatat                                                                    >  2:35103/1‑139 (MQ=255)
                                                   tGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTatat                                                                    >  1:33610/1‑139 (MQ=255)
                                                   tGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATCCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTatat                                                                    >  2:310308/1‑139 (MQ=255)
                                                    gCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATAtt                                                                   <  1:176043/139‑1 (MQ=255)
                                                        catAAACCACACCGTAGTTACGGCCGTAATCGAAAGATCCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCa                                                               <  1:264404/139‑1 (MQ=255)
                                                        catAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCa                                                               <  1:579750/139‑1 (MQ=255)
                                                           aaaCCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTg                                                            >  1:1000154/1‑139 (MQ=255)
                                                               cacaCCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGgcgc                                                                                                                             <  1:196187/70‑1 (MQ=255)
                                                               cacaCCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGgcgc                                                                                                                             >  2:196187/1‑70 (MQ=255)
                                                                 cacCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCa                                                                                            <  1:689821/101‑1 (MQ=255)
                                                                 cacCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCa                                                                                            >  2:689821/1‑101 (MQ=255)
                                                                       aGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGt                                                <  2:1000154/139‑1 (MQ=255)
                                                                         ttACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTAccc                                                                                >  1:141802/1‑105 (MQ=255)
                                                                         ttACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTAccc                                                                                <  2:141802/105‑1 (MQ=255)
                                                                              gCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCa                                                               <  1:1212300/117‑1 (MQ=255)
                                                                              gCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCa                                                               >  2:1212300/1‑117 (MQ=255)
                                                                              gCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCg                                         >  1:384292/1‑139 (MQ=255)
                                                                              gCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCg                                         >  1:353677/1‑139 (MQ=255)
                                                                                cGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGAc                                                          >  1:1005384/1‑120 (MQ=255)
                                                                                cGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGAc                                                          <  2:1005384/120‑1 (MQ=255)
                                                                                   aaTCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGAAtt                                    >  2:1217188/1‑139 (MQ=255)
                                                                                         aaGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGAATTGATTTg                              >  1:1152237/1‑139 (MQ=255)
                                                                                             aCCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTAc                                                                                                                   <  2:1168473/50‑1 (MQ=255)
                                                                                             aCCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTAc                                                                                                                   >  1:1168473/1‑50 (MQ=255)
                                                                                              ccAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGa                                       >  2:571099/1‑125 (MQ=255)
                                                                                              ccAACGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGa                                       <  1:571099/125‑1 (MQ=255)
                                                                                                aaCGTCAGCGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGAATTGATTTGAGTTTcc                       <  2:1169931/139‑1 (MQ=255)
                                                                                                        cGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCag                                                                                           <  1:199266/63‑1 (MQ=255)
                                                                                                        cGTATTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCag                                                                                           >  2:199266/1‑63 (MQ=255)
                                                                                                           aTTTAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGAATTGATTTGAGTTTCCCCTTTAAAAcc            <  2:353677/139‑1 (MQ=255)
                                                                                                             ttAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTgg                                                                             >  2:107110/1‑72 (MQ=255)
                                                                                                             ttAAGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGAATTGATTTGAGTTTCCCCTTTAAAACCaa          >  1:122519/1‑139 (MQ=255)
                                                                                                             gtAAGACCCGCGAATGCCAGGCGCGGTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTgg                                                                             <  1:107110/71‑1 (MQ=255)
                                                                                                               aaGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGAATTGATTTGAGTTTCCCCTTTAAAACCAAGa        <  1:470279/139‑1 (MQ=255)
                                                                                                                aGACCCGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGAATTGATTTGAGTTTCCCCTTTAAAACCAAGAc       <  2:122519/139‑1 (MQ=255)
                                                                                                                aGACCCGCGAATCCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGAATTGATTTGAGTTTCCCCTTTAAAACCAAGAc       <  1:310308/139‑1 (MQ=255)
                                                                                                                    ccGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTAcc                                                                                 >  2:253427/1‑61 (MQ=255)
                                                                                                                    ccGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTAcc                                                                                 <  1:253427/61‑1 (MQ=255)
                                                                                                                    ccGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCa                                                               >  1:1124495/1‑79 (MQ=255)
                                                                                                                    ccGCGAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCa                                                               <  2:1124495/79‑1 (MQ=255)
                                                                                                                     cgcgAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGt                                                                         <  1:269539/68‑1 (MQ=255)
                                                                                                                     cgcgAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGt                                                                         >  2:269539/1‑68 (MQ=255)
                                                                                                                     cgcgAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGt                                                >  2:616048/1‑93 (MQ=255)
                                                                                                                     cgcgAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGt                                                <  1:616048/93‑1 (MQ=255)
                                                                                                                     cgcgAATGCCAGGCGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGAATTGATTTGAGTTTCCCCTTTAAAACCAAGACGGGCa  >  1:1104829/1‑139 (MQ=255)
                                                                                                                                 |                                                                                                                              
GCTGTATGCAGTATCACCACCAAATTCTGGCAGCATATCGGTGTAACCCAGTGCATCATAAACCACACCGTAGTTACGGCCGTAATCGAAAGAACCAACGTCAGCGTATTTAAGACCCGCGAATGCCAGACGCGTTTTGTTACCAGTTTGAGCGTCAGCGCCTTCAGAGTTGTTACCCTGGAAGTTATATTCCCACTGACCATAACCGGTCAGATCGGAATTGATTTGAGTTTCCCCTTTAAAACCAAGACGGGCA  >  NC_000913/986542‑986797

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A