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 F1 I2 R1 780 68.3 3343050 93.5% 3125751 102.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,728,118 (C)8→9 coding (1254/1455 nt) xylB ← xylulokinase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,728,1101.C97.6% 137.4 / NA 41D421G (GAT→GGT) xylBxylulokinase
Reads supporting (aligned to +/- strand):  ref base . (0/0);  major base C (18/22);  minor base A (1/0);  total (19/22)
Fisher's exact test for biased strand distribution p-value = 4.63e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGCTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAT‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATGCACGACATCCA  >  NC_000913/3727972‑3728242
                                                                                                                                            |                                                                                                                                     
ggCTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAt                                                                                                                                        >  2:871246/1‑139 (MQ=255)
ggCTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAt                                                                                                                                        >  1:313087/1‑139 (MQ=255)
ggCTGAGAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGTTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAt                                                                                                                                        >  1:1523849/1‑139 (MQ=255)
     aTAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAT‑‑ccccc                                                                                                                                 >  1:1383701/1‑139 (MQ=255)
       aaGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAT‑‑ccccccc                                                                                                                               <  2:313087/139‑1 (MQ=255)
            gCATAACGCTGCGCATCTGTTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAT‑‑cccccccccgta                                                                                                                          <  1:1529995/139‑5 (MQ=255)
            gCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAT‑‑cccccccccgta                                                                                                                          <  2:195454/139‑5 (MQ=255)
               tAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACgg                                                                                                                        >  1:485531/1‑139 (MQ=255)
               tAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAT‑‑cccccccccgtac                                                                                                                         <  1:1434359/137‑6 (MQ=255)
               tAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAT‑‑cccccccccgtac                                                                                                                         >  2:1434359/1‑132 (MQ=255)
                 aCGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTa                                                                                                                      >  1:1469968/1‑139 (MQ=255)
                    cTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATc                                                                                                                   <  2:1383701/139‑1 (MQ=255)
                            cTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAACCGAgctgct                                                                                                           <  2:349937/139‑1 (MQ=255)
                                tAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGAcc                                                                                                       <  1:871246/139‑1 (MQ=255)
                                       gACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGata                                                                                                <  2:485531/139‑1 (MQ=255)
                                            ttCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAT‑‑cccc                                                                                                                                  >  1:520182/1‑99 (MQ=255)
                                            ttCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAT‑‑cccc                                                                                                                                  <  2:520182/99‑1 (MQ=255)
                                                      aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAg                                                                                                                >  1:620171/1‑108 (MQ=255)
                                                      aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAg                                                                                                                <  2:620171/108‑1 (MQ=255)
                                                      aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGCTATCCGCCAGCATCTGa                                                                                 >  1:920814/1‑139 (MQ=255)
                                                      aGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGa                                                                                 >  1:391041/1‑139 (MQ=255)
                                                        ttGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACg                                                                               <  2:1257150/139‑1 (MQ=255)
                                                                            gCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGcgccc                                                           >  2:281784/1‑139 (MQ=255)
                                                                             cGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTAc                                                                        <  2:154508/125‑1 (MQ=255)
                                                                             cGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTAc                                                                        >  1:154508/1‑125 (MQ=255)
                                                                              gATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGcgccccg                                                         <  2:391041/139‑1 (MQ=255)
                                                                                      tGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAAt                                                 <  2:1469968/139‑1 (MQ=255)
                                                                                      tGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAAt                                                 <  1:281784/139‑1 (MQ=255)
                                                                                      tGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAAt                                                 <  2:1070123/139‑1 (MQ=255)
                                                                                        gATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGc                                                                              >  1:1219579/1‑108 (MQ=255)
                                                                                        gATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGc                                                                              <  2:1219579/108‑1 (MQ=255)
                                                                                         aTTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCCCTGAAATCCGCCAGCACCTGACGCCAGAACTCACTCCGCGCCCCCCCCCCaacaca                                              >  1:1070123/1‑135 (MQ=255)
                                                                                            cgccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAT‑‑gccccccccg                                                                                                                            >  2:753676/1‑55 (MQ=255)
                                                                                            cgccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCGGGCCCCA‑CAT‑‑cccccccccg                                                                                                                            <  1:753676/57‑3 (MQ=255)
                                                                                             gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGGTATCCGCCAGCATCTGACGCCATACCTCACTACGCGCCCCGCCCCCAATCAAcaga                                          >  1:1302924/1‑136 (MQ=255)
                                                                                             gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCt                                                                                   <  1:319257/98‑1 (MQ=255)
                                                                                             gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCt                                                                                   >  2:319257/1‑98 (MQ=255)
                                                                                             gccgcGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTa                                          >  1:556385/1‑139 (MQ=255)
                                                                                               cgcgATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGAc                                                                                                        >  2:806992/1‑75 (MQ=255)
                                                                                               cgcgATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGAc                                                                                                        <  1:806992/75‑1 (MQ=255)
                                                                                                  gATCTGCGCCCGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATA‑CCCCCCCCGTACGGCAATCAAGCACCTGATCGCTGGTATCCGCCCGCATCCGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACt                                     >  1:1645099/1‑139 (MQ=255)
                                                                                                   aTCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGAcc                                                                               >  2:616107/1‑96 (MQ=255)
                                                                                                   aTCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATCCCCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACg                                                                               <  1:616107/97‑1 (MQ=255)
                                                                                                     cTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTg                                  <  1:1549152/139‑1 (MQ=255)
                                                                                                        cgcCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAg                                                                                                                <  1:284579/58‑1 (MQ=255)
                                                                                                        cgcCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAg                                                                                                                >  2:284579/1‑58 (MQ=255)
                                                                                                         gcCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGcgccccgc                                                        <  2:168650/113‑1 (MQ=255)
                                                                                                         gcCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGcgccccgc                                                        >  1:168650/1‑113 (MQ=255)
                                                                                                              ccTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTg                                  >  2:999375/1‑130 (MQ=255)
                                                                                                              ccTTGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTg                                  <  1:999375/130‑1 (MQ=255)
                                                                                                                ttGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAg                                                                                                                <  1:1454772/50‑1 (MQ=255)
                                                                                                                ttGCTGCGCCCAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAg                                                                                                                >  2:1454772/1‑50 (MQ=255)
                                                                                                                     gcgcCCAGCGCGGGCCCAACCCC‑‑CCCCCCCCGTCCGGTAATCGAGCTTCGTACCGCTGATATCCGCCAGCAACTGACGCCAATACTCACTTCGCGCGCCGCCCCCAGATGTCTTTACACTTTGCGGTTTAAGACCGCAg                  <  1:1266792/139‑1 (MQ=255)
                                                                                                                        cccAGTGCTGGCCCCA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCa               <  2:1523849/139‑1 (MQ=255)
                                                                                                                                     ccA‑CATC‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATGCACGACATCCa  <  2:556385/139‑1 (MQ=255)
                                                                                                                                            |                                                                                                                                     
GGCTGATAAGCGGCATAACGCTGCGCATCTGGTAGATGCGACTGTTCTAACGGTAGTTGCGGCAACAATTCAATGAGCGATTTCTCTGGATTCGCCGCGATCTGCGCCAGCCTTGCTGCGCCCAGTGCTGGCCCCA‑CAT‑‑CCCCCCCCGTACGGTAATCGAGCTGCTGACCGCTGATATCCGCCAGCATCTGACGCCAGTACTCACTACGCGCCCCGCCCCCAATCAACGTAACACTTTGCGGTTTAATACCGCAGGCATGCACGACATCCA  >  NC_000913/3727972‑3728242

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A