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
A7 F1 I1 R1 776 60.0 3074904 90.1% 2770488 104.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 2,220,195 A→G F599L (TTC→CTC)  bglX ← beta‑D‑glucoside glucohydrolase, periplasmic

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009132,220,1950AG97.0% 217.0 / ‑2.8 67F599L (TTC→CTC) bglXbeta‑D‑glucoside glucohydrolase, periplasmic
Reads supporting (aligned to +/- strand):  ref base A (1/1);  new base G (36/29);  total (37/30)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.46e-01

AACGGATACAACGCCCCGTTAGCTTCATCAAAATAACGCGAAGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAAGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCATCAGCCTGCTGATCTTCTTTCACCAGCGCCAG  >  NC_000913/2220065‑2220327
                                                                                                                                  |                                                                                                                                    
aaCGGATACAACGCCCCGTTAGCTTCATCAAAATAACGCGAAGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTg                                                                                                                              >  1:468013/1‑139 (MQ=255)
aaCGGATACAACGCCCCGTTAGCTTCATCAAAATAACGCGAAGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTg                                                                                                                              >  2:176391/1‑139 (MQ=255)
   ggATACAACGCCCCGTTAGCTTCATCAAAATAACGCGAAGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCa                                                                                                                           <  2:419956/139‑1 (MQ=255)
             ccccGTTAGCTTCATCAAAATAACGCGAAGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGa                                                                                                                 <  2:1063262/139‑1 (MQ=255)
                          atcaAAATAACGCGAAGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCg                                                                                                    <  1:266053/139‑1 (MQ=255)
                          atcaAAATAACGCGAAGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCg                                                                                                    <  2:776279/139‑1 (MQ=255)
                          atcaAAATAACGCGAAGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCg                                                                                                    <  2:1447203/139‑1 (MQ=255)
                            caAAATAACGCGAAGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGcc                                                                                                  <  1:176391/139‑1 (MQ=255)
                             aaaaTAACGCGAAGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCa                                                                                                 <  1:1299507/139‑1 (MQ=255)
                                   aCGCGAAGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAAt                                                                                           <  2:468013/139‑1 (MQ=255)
                                         aGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCg                                                                                     >  2:416869/1‑139 (MQ=255)
                                         aGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCg                                                                                     >  2:1241797/1‑139 (MQ=255)
                                                   ttCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGa                                                                                                                 >  2:857930/1‑101 (MQ=255)
                                                   ttCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGa                                                                                                                 <  1:857930/101‑1 (MQ=255)
                                                     cGGCTTGTCGGCATTGTACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGAAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTa                                                                         >  2:1025196/1‑139 (MQ=255)
                                                     cGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTa                                                                         >  1:116446/1‑139 (MQ=255)
                                                       gCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTAcc                                                                       >  1:772737/1‑139 (MQ=255)
                                                        cTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCg                                                                      <  1:877135/139‑1 (MQ=255)
                                                                cATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGt                                                              <  1:325432/139‑1 (MQ=255)
                                                                          gCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAAc                                                    >  1:335761/1‑139 (MQ=255)
                                                                          gCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAAc                                                    >  2:582875/1‑139 (MQ=255)
                                                                           cGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAAcc                                                   >  1:104103/1‑139 (MQ=255)
                                                                             aCCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGa                                                                                                                 <  1:249008/75‑1 (MQ=255)
                                                                             aCCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGa                                                                                                                 >  2:249008/1‑75 (MQ=255)
                                                                             aCCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAg                                                 >  1:1198549/1‑139 (MQ=255)
                                                                             aCCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAg                                                 >  1:480883/1‑139 (MQ=255)
                                                                               cGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTAc                                                                        >  1:872287/1‑114 (MQ=255)
                                                                               cGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTAc                                                                        <  2:872287/114‑1 (MQ=255)
                                                                                 gTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGcc                                                                                                  <  2:149459/86‑1 (MQ=255)
                                                                                 gTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGcc                                                                                                  >  1:149459/1‑86 (MQ=255)
                                                                                     tCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAg                                         <  2:1198549/139‑1 (MQ=255)
                                                                                         aTGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGAc                                                                                                                <  1:1123078/64‑1 (MQ=255)
                                                                                         aTGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGAc                                                                                                                >  2:1123078/1‑64 (MQ=255)
                                                                                         aTGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATTGCCAAACAATACATCGGCAATTGCATTACCGTCTTCAGTCCCCGCAAACCAGGTTTCCAGAATc                                     >  2:1281192/1‑139 (MQ=255)
                                                                                           ggCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGc                                   >  1:1138572/1‑139 (MQ=255)
                                                                                            gCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGa                                                                                                                 >  1:1096530/1‑60 (MQ=255)
                                                                                            gCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGa                                                                                                                 <  2:1096530/60‑1 (MQ=255)
                                                                                            gCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCa                                  >  2:1521439/1‑139 (MQ=255)
                                                                                            gCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGGTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCa                                  >  2:1437415/1‑139 (MQ=255)
                                                                                              tGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCg                                                                                                    <  1:315874/71‑1 (MQ=255)
                                                                                              tGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCg                                                                                                    >  2:315874/1‑71 (MQ=255)
                                                                                                         gggATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCATCAGCCTGCTGAt                     <  1:1241797/139‑1 (MQ=255)
                                                                                                         gggATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCATCAGCCTGCTGAt                     <  2:335761/139‑1 (MQ=255)
                                                                                                          ggATCTGCCCGACAGAGCGCGGGAAGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCg                                                         <  1:1272684/102‑1 (MQ=255)
                                                                                                          ggATCTGCCCGACAGAGCGCGGGAAGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCg                                                         >  2:1272684/1‑102 (MQ=255)
                                                                                                          ggATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCATCAGCCTGCTGAtc                    >  2:170249/1‑139 (MQ=255)
                                                                                                          ggATCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCATCAGCCTGCTGAtc                    >  1:1407305/1‑139 (MQ=255)
                                                                                                            aTCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCATCAGCctg                          >  1:1461813/1‑131 (MQ=255)
                                                                                                            aTCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCATCAGCctg                          <  2:1461813/131‑1 (MQ=255)
                                                                                                             tCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGa                                                                                                                 <  2:1447788/43‑1 (MQ=255)
                                                                                                             tCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGa                                                                                                                 >  1:1447788/1‑43 (MQ=255)
                                                                                                             tCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAAt                                                                                                      <  1:284716/54‑1 (MQ=255)
                                                                                                             tCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAAt                                                                                                      >  2:284716/1‑54 (MQ=255)
                                                                                                             tCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGaa                                       <  1:448844/117‑1 (MQ=255)
                                                                                                             tCTGCCCGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGaa                                       >  2:448844/1‑117 (MQ=255)
                                                                                                             tCTGCCCGACAGAACGCCGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCATCAGCCTGCTGAtcttc                 >  1:959054/1‑139 (MQ=255)
                                                                                                                 cccGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGt                                                              <  1:562431/90‑1 (MQ=255)
                                                                                                                 cccGACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGt                                                              >  2:562431/1‑90 (MQ=255)
                                                                                                                    gACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGt                                               >  2:1338347/1‑102 (MQ=255)
                                                                                                                    gACAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGt                                               <  1:1338347/102‑1 (MQ=255)
                                                                                                                      cAGAACGCGGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCGCGCAAACCAGGTTTCCAGAATCGCATCAGCCTGCTGATCTTCTTTCAccag        >  2:1023681/1‑139 (MQ=255)
                                                                                                                           cgcgGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGcc                                                                                                  <  2:400376/44‑1 (MQ=255)
                                                                                                                           cgcgGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGcc                                                                                                  >  1:400376/1‑44 (MQ=255)
                                                                                                                           cgcgGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACAt                                                                                       <  1:550019/55‑1 (MQ=255)
                                                                                                                           cgcgGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACAt                                                                                       >  2:550019/1‑55 (MQ=255)
                                                                                                                           cgcgGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCATCAGCCTGCTGATCTTCTTTCAccagcgcca   >  2:233724/1‑139 (MQ=255)
                                                                                                                            gcgGGAGGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCATCAGCCTGCTGATCTTCTTTCAccagcgccag  <  2:104103/139‑1 (MQ=255)
                                                                                                                              gggagggaCATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTc                                                                 <  2:694054/74‑1 (MQ=255)
                                                                                                                              gggagggaCATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTc                                                                 >  1:694054/1‑74 (MQ=255)
                                                                                                                                  |                                                                                                                                    
AACGGATACAACGCCCCGTTAGCTTCATCAAAATAACGCGAAGTGTATTTGTTCGGCTTGTCGGCATTATACGGGCGACCGGTATTCAGATGGCTGTAGTACACCGGGATCTGCCCGACAGAACGCGGGAAGGACATTGGCAGCTTGCCGGACGGGTTGTAATCGCCAAACAATACATCGGCAATTGCATTACCGCCTTCAGTCCCCGCAAACCAGGTTTCCAGAATCGCATCAGCCTGCTGATCTTCTTTCACCAGCGCCAG  >  NC_000913/2220065‑2220327

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 25 ≤ 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