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
A25 F36 I0 R2 1302 104.9 4551290 96.3% 4382892 111.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 2,279,708 A→T 9.4% L18Q (CTG→CAG)  bcr ← bicyclomycin/cysteine/sulfonamide efflux transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,279,7080AT 9.4% 212.9 / 11.7 64L18Q (CTG→CAG) bcrbicyclomycin/cysteine/sulfonamide efflux transporter
Reads supporting (aligned to +/- strand):  ref base A (28/30);  new base T (3/3);  total (31/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.22e-01

CGTAGATTAACTGCCCCAACGCAAAGCCCAGAATATAAGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCTGGCAATTTCTTCTTCAGTTAACGGA  >  NC_000913/2279565‑2279824
                                                                                                                                               |                                                                                                                    
cGTAGATTAACTGCCCCAACGCAAAGCCCAGAATATAAGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCcagcag                                                                                                                  >  4:324971/1‑148 (MQ=255)
               ccAACGCAAAGCCCAGACTACAAGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAgg                                                                                                                 <  3:198115/134‑1 (MQ=255)
               ccAACGCAAAGCCCAGAATATTAGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAgg                                                                                                                 >  4:198115/1‑134 (MQ=255)
                   cGCAAAGCCCAGAATATAAGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATa                                                                                               <  3:324971/148‑1 (MQ=255)
                            cAGAATATAAGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAacgac                                                                                      >  4:793355/1‑148 (MQ=255)
                               aaTATAAGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATa                                                                                               >  2:727257/1‑136 (MQ=255)
                               aaTATAAGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATa                                                                                               <  1:727257/136‑1 (MQ=255)
                                    aaGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCaa                                                                                                             >  2:950559/1‑117 (MQ=255)
                                    aaGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCaa                                                                                                             <  1:950559/117‑1 (MQ=255)
                                     aGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCcagc                                                                                                                    >  3:434003/1‑109 (MQ=255)
                                     aGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCcagc                                                                                                                    <  4:434003/109‑1 (MQ=255)
                                     aGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGt                                                                             >  4:106229/1‑148 (MQ=255)
                                          tGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGggt                                                                        <  3:106229/148‑1 (MQ=255)
                                                 cATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTcaca                                                                 >  1:541649/1‑148 (MQ=255)
                                                   tCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGc                                                                                >  4:295060/1‑131 (MQ=255)
                                                   tCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGc                                                                                <  3:295060/131‑1 (MQ=255)
                                                   tCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAAc                                                               >  2:234271/1‑148 (MQ=255)
                                                         tACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTc                                                         <  1:234271/148‑1 (MQ=255)
                                                           cTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTcaca                                                                 >  2:843890/1‑138 (MQ=255)
                                                           cTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTcaca                                                                 <  1:843890/138‑1 (MQ=255)
                                                            tGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTg                                                      >  3:431768/1‑148 (MQ=255)
                                                             gCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCTGCTGGCCa                                                                                                              >  3:804684/1‑91 (MQ=255)
                                                             gCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCTGCTGGCCa                                                                                                              <  4:804684/91‑1 (MQ=255)
                                                             gCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACa                                                                                                  >  2:634235/1‑103 (MQ=255)
                                                             gCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACa                                                                                                  <  1:634235/103‑1 (MQ=255)
                                                              cccGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGaa                                                    >  3:136401/1‑148 (MQ=255)
                                                                         gCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGaaa                                         <  3:793355/148‑1 (MQ=255)
                                                                         gCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGaaa                                         <  2:541649/148‑1 (MQ=255)
                                                                         gCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGaaa                                         <  4:136401/148‑1 (MQ=255)
                                                                             aaCTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCa                                               <  3:193312/138‑1 (MQ=255)
                                                                             aaCTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCa                                               >  4:193312/1‑138 (MQ=255)
                                                                             aaCTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGtt                                     >  3:215112/1‑148 (MQ=255)
                                                                             aaCTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGtt                                     <  4:215112/148‑1 (MQ=255)
                                                                                     tGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCTGCTGGCCatg                                                                                                            >  2:708937/1‑67 (MQ=255)
                                                                                     tGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCTGCTGGCCatg                                                                                                            <  1:708937/69‑3 (MQ=255)
                                                                                      gAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACAACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGc                            >  2:113650/1‑148 (MQ=255)
                                                                                       aaaTTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGa                                                                                                          <  4:456045/69‑1 (MQ=255)
                                                                                       aaaTTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGa                                                                                                          >  3:456045/1‑69 (MQ=255)
                                                                                         aTTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCGGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGggtg                                                                       <  4:448905/102‑1 (MQ=255)
                                                                                         aTTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATAAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGggtg                                                                       >  3:448905/1‑102 (MQ=255)
                                                                                          ttACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCTGCTGGCCa                                                                                                              <  3:258711/62‑1 (MQ=255)
                                                                                          ttACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCTGCTGGCCa                                                                                                              >  4:258711/1‑62 (MQ=255)
                                                                                                gTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCTGGCAATttc                  <  1:1026910/148‑1 (MQ=255)
                                                                                                  aGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCTGGCAATttctt                <  4:431768/148‑1 (MQ=255)
                                                                                                            gATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAATTTAga                                  <  2:800672/120‑1 (MQ=255)
                                                                                                            gATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAga                                  >  1:800672/1‑120 (MQ=255)
                                                                                                              tACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGaa                                                    >  4:56810/1‑100 (MQ=255)
                                                                                                              tACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGaa                                                    <  3:56810/100‑1 (MQ=255)
                                                                                                              tACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCt                           >  1:1119917/1‑125 (MQ=255)
                                                                                                              tACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCt                           <  2:1119917/125‑1 (MQ=255)
                                                                                                                cATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACAACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCTGGCAATTTCTTCTTCAGTTAACGGa  <  1:113650/148‑1 (MQ=255)
                                                                                                                  tatCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAacg                                                                                        <  3:744377/60‑1 (MQ=255)
                                                                                                                  tatCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAacg                                                                                        >  4:744377/1‑60 (MQ=255)
                                                                                                                    tCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCTGGCa                       <  2:124385/123‑1 (MQ=255)
                                                                                                                    tCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCTGGCa                       >  1:124385/1‑123 (MQ=255)
                                                                                                                        tCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGt                                                                             <  3:812987/65‑1 (MQ=255)
                                                                                                                        tCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGt                                                                             >  4:812987/1‑65 (MQ=255)
                                                                                                                        tCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCAt                                              <  2:1026519/96‑1 (MQ=255)
                                                                                                                        tCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCAt                                              >  1:1026519/1‑96 (MQ=255)
                                                                                                                        tCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCTGGCAATTTCTTCTTCAGTTaa      <  4:344462/136‑1 (MQ=255)
                                                                                                                        tCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCTGGCAATTTCTTCTTCAGTTaa      >  3:344462/1‑136 (MQ=255)
                                                                                                                                    tCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCa                                               >  1:783364/1‑83 (MQ=255)
                                                                                                                                    tCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCa                                               <  2:783364/83‑1 (MQ=255)
                                                                                                                                     cAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGggtggt                                                                     >  4:697457/1‑60 (MQ=255)
                                                                                                                                     cAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGggtggt                                                                     <  3:697457/60‑1 (MQ=255)
                                                                                                                                           ggCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGc                                                                                <  4:431714/43‑1 (MQ=255)
                                                                                                                                           ggCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGc                                                                                >  3:431714/1‑43 (MQ=255)
                                                                                                                                               agcagGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCTGGCAATttctt                >  1:49081/1‑103 (MQ=255)
                                                                                                                                               agcagGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCTGGCAATttctt                <  2:49081/103‑1 (MQ=255)
                                                                                                                                               |                                                                                                                    
CGTAGATTAACTGCCCCAACGCAAAGCCCAGAATATAAGTACTGAGGGTCATCTGCGTACTGCCCGCCGGTACGCCAAACTGCGCTGAAATTACCGGTAGCGCGGGCAGATACATATCAATCGACAGCGGCATCAACATGGCCAGCAGGCCAAGGATAAAAACAATAGCAAACGACGAATGCTGTCGGGTGGTCACAACGGGCTCCTGAAAGTCATTGAAAAGTTAGACGACGCTGGCAATTTCTTCTTCAGTTAACGGA  >  NC_000913/2279565‑2279824

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A