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
A2 F999 I1 R1 226 132.7 9745491 85.7% 8351885 75.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,957,124 +G intergenic (+58/+26) ilvC → / ← ppiC ketol‑acid reductoisomerase/peptidyl‑prolyl cis‑trans isomerase C

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,957,1231.G97.5% 181.1 / ‑1.3 81intergenic (+57/+27)ilvC/ppiCketol‑acid reductoisomerase/peptidyl‑prolyl cis‑trans isomerase C
Reads supporting (aligned to +/- strand):  ref base . (2/0);  new base G (35/44);  total (37/44)
Fisher's exact test for biased strand distribution p-value = 2.06e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

TGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGA‑‑CTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑GCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATCCGAACTGGG  >  NC_000913/3957051‑3957193
                                                                             |                                                                      
tGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑g                                                                       >  1:4414096/1‑76 (MQ=18)
 gCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑gg                                                                      <  2:2305205/76‑2 (MQ=17)
 gCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑gg                                                                      <  2:3756495/76‑2 (MQ=17)
 gCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑gg                                                                      >  1:2133084/1‑75 (MQ=17)
  cTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑ggc                                                                     <  1:4433576/76‑3 (MQ=17)
   tGTTGCGGGTTAAGGGCGCGCTGATGCCCTCACCCCGACCCGCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑ggcc                                                                    >  1:703250/1‑73 (MQ=17)
      tGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtc                                                                  >  2:1941298/1‑76 (MQ=14)
      tGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtc                                                                  <  2:2925065/76‑1 (MQ=14)
       gCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtct                                                                 <  2:1612000/76‑1 (MQ=14)
       gCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtct                                                                 <  2:2368892/76‑1 (MQ=14)
       gCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtct                                                                 >  2:2722957/1‑76 (MQ=14)
       gCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtct                                                                 >  1:955500/1‑76 (MQ=14)
        cGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtctc                                                                >  1:2074472/1‑76 (MQ=14)
        cGGGTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTtctc                                                                <  1:2565759/76‑1 (MQ=14)
         gggTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTcc                                                               >  1:1461407/1‑76 (MQ=14)
         gggTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTcc                                                               >  1:2235355/1‑76 (MQ=14)
         gggTTAAGTGCGCGCTGATGACCTCACACCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTcc                                                               >  1:901981/1‑76 (MQ=14)
          ggTTAAGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCt                                                              <  2:3257407/76‑1 (MQ=14)
          ggTTAAGTGCGCGCTGATGCCCGCACCCCGACCCTCTCCCACAGGGAGAGGGAGCACACACT‑C‑AAGGCCTTCTCCt                                                              <  2:703250/76‑1 (MQ=14)
             tAAGTGCGCGCTGATGCCCTCTCCCCGACCCTCTCCCACAGGTAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGga                                                           <  1:2589307/76‑1 (MQ=14)
               aGTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACTCC‑AG‑GCCTTCTCCTGgaga                                                         >  1:3318988/1‑76 (MQ=14)
                gTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGaa                                                        <  2:4635747/76‑1 (MQ=14)
                gTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGaa                                                        <  2:3931756/76‑1 (MQ=14)
                gTGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGaa                                                        <  2:426167/76‑1 (MQ=14)
                 tGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAg                                                       <  2:1289684/76‑1 (MQ=14)
                 tGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAg                                                       <  1:1973819/76‑1 (MQ=17)
                 tGCGCGCTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCCTCTCCTGGAGAAg                                                       >  2:990502/1‑76 (MQ=14)
                 ggcgcgcTGATGCCCTACCCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAg                                                       <  2:2198243/75‑1 (MQ=14)
                   cgcgcTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGCAGGc                                                     >  2:1746703/1‑76 (MQ=14)
                    gcgcTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑CAAA‑GCCTGCTCCTGGAGAAGGcc                                                    >  1:883833/1‑76 (MQ=17)
                    gcgcTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGcc                                                    >  1:3941187/1‑76 (MQ=17)
                    gcgcTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGcc                                                    >  2:1309370/1‑76 (MQ=17)
                     cgcTGATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCt                                                   >  1:1166489/1‑76 (MQ=17)
                      tcggATGCCCTGACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCtt                                                  <  1:700137/73‑1 (MQ=17)
                      gcTGATGCCCTCACCGCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCtt                                                  <  1:956227/76‑1 (MQ=17)
                         gATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCt                                               <  1:4145504/76‑1 (MQ=18)
                         gATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCt                                               <  2:832927/76‑1 (MQ=18)
                         gATGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCt                                               >  1:1322609/1‑76 (MQ=18)
                          aTGCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTa                                              <  2:2774749/76‑1 (MQ=18)
                            gCCCTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTAtt                                            <  2:1682834/76‑1 (MQ=18)
                              ccTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAg                                          >  1:3385060/1‑76 (MQ=21)
                               cTCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGt                                         >  1:3049342/1‑76 (MQ=21)
                                tCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGtt                                        >  2:4365379/1‑76 (MQ=21)
                                tCACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGtt                                        >  1:1918893/1‑76 (MQ=21)
                                ccACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGtt                                        <  2:684935/75‑1 (MQ=21)
                                 cACCCCGACCCTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTg                                       >  1:1400570/1‑76 (MQ=25)
                                        accctctCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACa                                <  1:1192640/73‑1 (MQ=38)
                                        accctctCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACa                                <  1:3965145/73‑1 (MQ=38)
                                        accctctCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACa                                >  1:2191565/4‑76 (MQ=38)
                                         ccctctCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAg                               >  2:1669039/3‑76 (MQ=38)
                                         ccctctCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAg                               <  1:2266195/74‑1 (MQ=38)
                                          cctctCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGc                              >  2:3087169/2‑76 (MQ=255)
                                          cctctCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGc                              <  2:1751870/75‑1 (MQ=255)
                                           ctctCCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGcc                             >  2:1483754/1‑75 (MQ=255)
                                            tctcCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCAc                            <  1:2320381/76‑1 (MQ=255)
                                            gctcCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCAc                            <  2:2296007/75‑1 (MQ=255)
                                             ctcCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCAcc                           >  2:3458080/1‑76 (MQ=255)
                                             ctcCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCAcc                           <  1:1941299/76‑1 (MQ=255)
                                              tcCCACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCt                          <  2:4224151/76‑1 (MQ=255)
                                                ccACAGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTa                        >  2:1012290/1‑76 (MQ=255)
                                                  acaGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAat                      <  1:3849552/76‑1 (MQ=255)
                                                  acaGGGAGAGGGAGAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAat                      >  2:1615497/1‑76 (MQ=255)
                                                    agggagagggagAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAatga                    >  2:365944/1‑76 (MQ=255)
                                                    agggagagggagAAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGGACAGCACCTTAatga                    >  2:726576/1‑76 (MQ=255)
                                                     gggagagggagaAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAatgat                   <  2:1380563/76‑1 (MQ=255)
                                                      ggagagggagaAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAatgatg                  >  1:3444256/1‑76 (MQ=255)
                                                         gagggagaAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGa               <  2:4041260/76‑1 (MQ=255)
                                                          agggagaAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGat              <  2:2319532/76‑1 (MQ=255)
                                                          agggagaAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGat              <  2:2467262/76‑1 (MQ=255)
                                                          agggagaAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGat              >  1:1962798/1‑76 (MQ=255)
                                                           gggagaAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGata             >  1:1984821/1‑76 (MQ=255)
                                                           gggagaAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGata             <  2:2877736/76‑1 (MQ=255)
                                                            ggagaAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGatat            <  2:3299150/76‑1 (MQ=255)
                                                             gagaAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATc           <  1:1509860/76‑1 (MQ=255)
                                                              agaAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATcc          <  2:2263968/76‑1 (MQ=255)
                                                              agaAAACACT‑C‑AAGGCCTGCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATcc          <  1:3748113/76‑1 (MQ=255)
                                                               gaAGACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATCCg         <  1:2122368/76‑1 (MQ=255)
                                                               gaAAACACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATCCg         >  1:586364/1‑76 (MQ=255)
                                                                 aaaCACT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATCCGaa       <  1:1341982/76‑1 (MQ=255)
                                                                   acacT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATCCGAACt     >  2:2441170/1‑76 (MQ=255)
                                                                    cacT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATCCGAACTg    <  2:1339943/76‑1 (MQ=255)
                                                                     acT‑C‑AAGGCCTTCTCCTGGCGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATCCGAACTgg   <  2:3280593/76‑1 (MQ=255)
                                                                     acT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATCCGAACTgg   >  2:3154763/1‑76 (MQ=255)
                                                                     acT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATCCGAACTgg   >  2:2475598/1‑76 (MQ=255)
                                                                     acT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATCCGAACTgg   <  2:1918892/76‑1 (MQ=255)
                                                                      cT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATCCGAACTggg  <  1:4814252/76‑1 (MQ=255)
                                                                      cT‑C‑AAGGCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTAAAGCACCTTAATGATGTGATATCCGAACTggg  >  2:182386/1‑76 (MQ=255)
                                                                             |                                                                      
TGCTGTTGCGGGTTAAGTGCGCGCTGATGCCCTCACCCCGA‑‑CTCTCCCACAGGGAGAGGGAGAAAACACT‑C‑AA‑GCCTTCTCCTGGAGAAGGCCTTGCTATTAGTTGCGGTACAGCACCTTAATGATGTGATATCCGAACTGGG  >  NC_000913/3957051‑3957193

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 11 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A