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
A6 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 312,540 C→G 20.5% L111L (CTG→CTC)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE312,5400CG20.5% 222.2 / 50.1 107L111L (CTG→CTC) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base C (43/42);  new base G (9/13);  total (52/55)
Fisher's exact test for biased strand distribution p-value = 4.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

Only 100 of 108 total aligned reads displayed.

CTGGATGATTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGATCTGCA  >  minE/312472‑312610
                                                                    |                                                                      
ctgGATGATTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAg                                                                      <  1:3829422/71‑1 (MQ=255)
   gatgatTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGttt                                                                   >  1:1551572/1‑71 (MQ=255)
   gatgatTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGt                                                                     <  1:2680066/69‑1 (MQ=255)
   gatgatTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGt                                                                     <  1:482382/69‑1 (MQ=255)
     tgatTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGt                                                                 >  1:2612182/1‑71 (MQ=255)
       atTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGtt                                                                <  1:3364271/70‑1 (MQ=255)
       atTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGtt                                                                <  1:2798951/70‑1 (MQ=255)
       atTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGtt                                                                <  1:3815906/70‑1 (MQ=255)
          tctcAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTg                                                             <  1:1227821/70‑1 (MQ=255)
              aaCGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGt                                                                 <  1:1126872/62‑1 (MQ=255)
              aaCGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCAc                                                          <  1:2075133/69‑1 (MQ=255)
                     atccccTGCTGCTGAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTg                                                 >  1:3585923/3‑71 (MQ=255)
                     aCCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTg                                                 >  1:240322/1‑71 (MQ=255)
                        ccTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTgcgc                                              >  1:2540559/1‑71 (MQ=255)
                        ccTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTgcgc                                              <  1:3724069/71‑1 (MQ=255)
                         cctgctgcTGAACCTCCTGCGGCAGCAACGTCGTGGCGAGCTGGAGTTTGTTCTGCa                                                           <  1:980077/55‑1 (MQ=255)
                         cctgctgcTGAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTTCa                                                           <  1:1587391/55‑1 (MQ=255)
                         cTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTg                                                             >  1:2035699/1‑55 (MQ=255)
                          ttGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGc                                                            <  1:604006/55‑1 (MQ=255)
                           tgctgcTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGa                                            >  1:1081387/1‑70 (MQ=255)
                           tgctgcTGAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGa                                            >  1:114107/1‑70 (MQ=255)
                            gctgctGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGaa                                                     >  1:3295860/1‑60 (MQ=255)
                            gctgctGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGa                                            <  1:923469/69‑1 (MQ=255)
                             ctgctgAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGatat                                         <  1:2940871/71‑1 (MQ=255)
                             ctgctgAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGatat                                         <  1:1885283/71‑1 (MQ=255)
                             ctgctgAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGata                                          <  1:3637246/70‑1 (MQ=255)
                             ctgctgAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCt                                                        <  1:1467817/56‑1 (MQ=255)
                             ctgctgAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCAGCACCTGCACTTGCGCGatat                                         <  1:2365335/71‑1 (MQ=255)
                              tgctgAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCt                                                              >  1:3035932/1‑49 (MQ=255)
                               gctgAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTgcgc                                              <  1:2523939/64‑1 (MQ=255)
                                ctgAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTg                                                 >  1:3640926/1‑60 (MQ=255)
                                ctgAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCg                                      >  1:734831/1‑71 (MQ=255)
                                ctgAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCg                                      >  1:1844797/1‑71 (MQ=255)
                                 tgAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGat                                           >  1:1130171/1‑65 (MQ=255)
                                 tgAACCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATcag                                      >  1:3561527/1‑68 (MQ=255)
                                  gAACTTCTTGCGGCAGCAACTGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGc                                     >  1:846843/1‑70 (MQ=255)
                                  gAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCa                                    >  1:265643/1‑71 (MQ=255)
                                  gAACTTCTTGCGGCAGCAACGGCATCGCCAGCAGCAGtttc                                                                  >  1:851633/1‑40 (MQ=255)
                                   aaCTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAAc                                                    <  1:2731992/54‑1 (MQ=255)
                                   aaCTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAAc                                                    <  1:9925/54‑1 (MQ=255)
                                   aaCTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGc                                     <  1:849499/69‑1 (MQ=255)
                                   aaCTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGc                                     <  1:854367/69‑1 (MQ=255)
                                   aaCTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGc                                     <  1:859700/69‑1 (MQ=255)
                                   aaCCTCCTGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATcagg                                     <  1:598713/69‑4 (MQ=19)
                                    aCTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCAt                                   >  1:3351000/1‑70 (MQ=255)
                                    aCTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCAt                                   >  1:3482184/1‑70 (MQ=255)
                                    aCTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCAt                                   >  1:2828559/1‑70 (MQ=255)
                                    aCTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATc                                  <  1:1409466/71‑1 (MQ=255)
                                     cttcttGCGGCAGCAACGGTATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCAt                                   >  1:2097907/1‑69 (MQ=255)
                                     cttcttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCt                                                  >  1:2098160/1‑54 (MQ=255)
                                       tcttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAg                                >  1:1851380/1‑70 (MQ=255)
                                        cttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAg                                <  1:1706671/69‑1 (MQ=255)
                                        cttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGt                               <  1:1148549/70‑1 (MQ=255)
                                        cttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGt                               <  1:1343322/70‑1 (MQ=255)
                                        cttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGt                               >  1:2067582/1‑70 (MQ=255)
                                        cttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGt                               <  1:2299812/70‑1 (MQ=255)
                                        cttGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTa                              >  1:10732/1‑71 (MQ=255)
                                         ctGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTTCACTTGCGCGATATCAGGATCGGt                               <  1:94435/68‑1 (MQ=255)
                                         ctGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGtcc                             >  1:2054891/2‑69 (MQ=255)
                                         ctGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGtcc                             >  1:1607135/2‑69 (MQ=255)
                                         ctGCGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGtc                              <  1:1321715/69‑2 (MQ=16)
                                           gCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTAc                             >  1:2540908/1‑69 (MQ=255)
                                           gCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTAc                             >  1:1500614/1‑69 (MQ=255)
                                            cGGCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTcccgg                          <  1:2303622/71‑3 (MQ=255)
                                            cGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAg                          <  1:3529200/71‑1 (MQ=255)
                                            cGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAg                          <  1:497714/71‑1 (MQ=255)
                                             ggCAGCAACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTCCCGGa                         >  1:484397/1‑71 (MQ=16)
                                              gcagcaTCGGCATCGCCAGCTGCAGTTTGTTGTGCACCTGAACCTGCGCGATATCCGCa                                    <  1:1993315/59‑1 (MQ=255)
                                              gcagcaACGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTCCCGGAc                        <  1:352053/71‑1 (MQ=16)
                                              gcagcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGAc                        <  1:503449/71‑1 (MQ=255)
                                              gcagcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGAc                        <  1:2401338/71‑1 (MQ=255)
                                               cagcaACGGCGTGGCGAGCTGGAGTTTGTTctgcacctgcac                                                    >  1:2626849/1‑42 (MQ=16)
                                               cagcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGAc                        >  1:315622/1‑70 (MQ=255)
                                               cagcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACt                       <  1:2520448/71‑1 (MQ=255)
                                                agcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATc                                  >  1:3313306/1‑59 (MQ=255)
                                                agcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACt                       >  1:3771861/1‑70 (MQ=255)
                                                agcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACt                       >  1:2187233/1‑70 (MQ=255)
                                                 gcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTc                      >  1:1205334/1‑70 (MQ=255)
                                                 gcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCa                     <  1:1549774/71‑1 (MQ=255)
                                                 gcaACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCa                     <  1:3253030/71‑1 (MQ=255)
                                                    aCGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAg                  >  1:962620/1‑71 (MQ=255)
                                                    aCGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAg                  >  1:684315/1‑71 (MQ=255)
                                                    aCGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAg                  >  1:689156/1‑71 (MQ=255)
                                                     cGGCGTGGCGAGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTCCCGGACTGGAAgg                 >  1:605973/1‑71 (MQ=255)
                                                     cGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAgg                 >  1:1005238/1‑71 (MQ=255)
                                                      ggCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGt                >  1:651667/1‑71 (MQ=255)
                                                       gCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTc               <  1:811430/71‑1 (MQ=255)
                                                        cATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCa              <  1:3712403/71‑1 (MQ=255)
                                                           cGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACt                       >  1:598168/1‑59 (MQ=255)
                                                            gCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCaaa                   >  1:3284913/1‑62 (MQ=255)
                                                             cgaGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTCCCGGACTGGAAGGTAAGGGta         <  1:2853999/69‑2 (MQ=12)
                                                             ccAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTg         <  1:1102180/71‑1 (MQ=255)
                                                              gaGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTCCCGGACTGGAAGGTAAGGGtaa        <  1:639487/70‑3 (MQ=255)
                                                              gaGCTGGAGTTTGTTCTGCACCTGCACTTGCGCGATATCAGGATCGGTCCCGGACTGGAAGGTAAGGGtaa        <  1:2916913/70‑3 (MQ=255)
                                                               aGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGAt       <  1:2366295/71‑1 (MQ=255)
                                                                 cTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCaa                    <  1:3310785/56‑1 (MQ=255)
                                                                   gCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAg                  >  1:1511077/1‑56 (MQ=255)
                                                                   gCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGATCTg    >  1:633201/1‑70 (MQ=255)
                                                                   gCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAAACTCAAAGGTCAGGGTGATCTg    >  1:2604417/1‑70 (MQ=255)
                                                                    cAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGATCTGCa  >  1:1096764/1‑71 (MQ=255)
                                                                    |                                                                      
CTGGATGATTTCTCAACGCTCACCCCTTGCTGCTGAACTTCTTGCGGCAGCAACGGCATCGCCAGCTGCAGTTTGTTCTGCACCTGAACCTGCGCGATATCCGCATCAGTACCAGACTCAAAGGTCAGGGTGATCTGCA  >  minE/312472‑312610

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A