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 F3 I0 R2 232 76.3 4135488 90.9% 3759158 60.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,513,416 T→C 22.3% F203S (TTT→TCT)  gltS → glutamate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,513,4160TC22.3% 170.5 / 48.9 85F203S (TTT→TCT) gltSglutamate transporter
Reads supporting (aligned to +/- strand):  ref base T (36/30);  new base C (11/8);  total (47/38)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.70e-01

GCGCTATCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCTGATTGCTA  >  minE/2513348‑2513484
                                                                    |                                                                    
gcgcTATCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGttt                                                                     >  1:295474/1‑70 (MQ=255)
gcgcTATCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGttt                                                                     >  1:1518859/1‑70 (MQ=255)
  gcTATCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGaa                                                                  <  1:3312171/71‑1 (MQ=255)
  gcTATCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGaa                                                                  <  1:3730296/71‑1 (MQ=255)
  gcTATCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTCTGa                                                                   >  1:1025683/1‑70 (MQ=255)
  gcTATCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTCTGa                                                                   >  1:199224/1‑70 (MQ=255)
     aTCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGaa                                                                  >  1:1342934/1‑68 (MQ=255)
     aTCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGaa                                                                  >  1:3669366/1‑68 (MQ=255)
     aTCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGaa                                                                  >  1:715051/1‑68 (MQ=255)
     aTCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGa                                                                   >  1:3290694/1‑67 (MQ=255)
      tCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGc                                                              >  1:3858163/1‑71 (MQ=255)
      tCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGc                                                              >  1:3740326/1‑71 (MQ=255)
      tCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGc                                                              >  1:373038/1‑71 (MQ=255)
      tCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGc                                                              >  1:447504/1‑71 (MQ=255)
      tCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGc                                                              >  1:639911/1‑71 (MQ=255)
      tCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGc                                                              >  1:2467265/1‑71 (MQ=255)
      tCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAg                                                               >  1:127482/1‑70 (MQ=255)
      tCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGc                                                              >  1:379952/1‑71 (MQ=255)
       cTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGaaaa                                                                >  1:3642927/1‑68 (MQ=255)
       cTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGaaaa                                                                >  1:3391597/1‑68 (MQ=255)
       cTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGaaaa                                                                >  1:1020884/1‑68 (MQ=255)
       cTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGaaaa                                                                >  1:982281/1‑68 (MQ=255)
       cTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGaaaa                                                                >  1:1193253/1‑68 (MQ=255)
        tGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCg                                                            >  1:1851196/1‑71 (MQ=255)
          gTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGa                                                          <  1:1814848/71‑1 (MQ=255)
          gTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGa                                                          <  1:158602/71‑1 (MQ=255)
             aaaCACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGa                                                          <  1:2524191/68‑1 (MQ=255)
             aaaCACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGAtgt                                                       >  1:1444946/1‑71 (MQ=255)
              aaCACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGAtg                                                        <  1:1136075/69‑1 (MQ=255)
               acacTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTgg                                                     >  1:1542225/1‑71 (MQ=255)
                cacTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTgg                                                     <  1:1077968/70‑1 (MQ=255)
                     caccacGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGc                                                <  1:1694848/70‑1 (MQ=255)
                     caccacGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGc                                                <  1:1157992/70‑1 (MQ=255)
                     caccacGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGc                                                <  1:1275922/70‑1 (MQ=255)
                     caccacGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGc                                                <  1:1838704/70‑1 (MQ=255)
                       ccacGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATg                                             <  1:3132318/71‑1 (MQ=255)
                         acGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGAt                                           >  1:647403/1‑71 (MQ=255)
                            ccGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCAc                                        >  1:2702557/1‑71 (MQ=255)
                               aaCGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTg                                                                    <  1:514843/40‑1 (MQ=255)
                                  ggTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCg                                                            <  1:2445794/45‑1 (MQ=255)
                                  ggTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCg                                                            <  1:229640/45‑1 (MQ=255)
                                   gTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGtt                                  >  1:1398234/1‑70 (MQ=255)
                                        ccGGATGACCAGGAAGTCCCGACGGCGTTTGaaaa                                                                >  1:1472475/1‑35 (MQ=255)
                                        ccGGATGACCAGGAAGTCCCGACGGCGTTTGaaaa                                                                >  1:3678606/1‑35 (MQ=255)
                                        ccGGATGACCAGGAAGTCCCGACGGCGTTTGaaaa                                                                >  1:4035413/1‑35 (MQ=255)
                                        ccGGATGACCAGGAAGTCCCGACGGCGTTTGaaaa                                                                >  1:2140779/1‑35 (MQ=255)
                                        ccGGATGACCAGGAAGTCCCGACGGCGTTTGaaaa                                                                >  1:2452016/1‑35 (MQ=255)
                                        ccGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCAt                                              >  1:419164/1‑53 (MQ=255)
                                        ccGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCAt                                              >  1:508949/1‑53 (MQ=255)
                                        ccGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCAc                                        >  1:1308906/1‑59 (MQ=255)
                                        ccGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGATGTGGGACGCATGATCAc                                        >  1:1859710/1‑59 (MQ=255)
                                        ccGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGATGTGGGACGCATGATCAc                                        >  1:1953571/1‑59 (MQ=255)
                                        ccGGATGACCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGATGTGGGACGCATGATCAc                                        >  1:2573940/1‑59 (MQ=255)
                                         cGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCt                            <  1:2700067/70‑1 (MQ=255)
                                               aCCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGa                      <  1:1658658/70‑1 (MQ=255)
                                               aCCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGa                      <  1:3155776/70‑1 (MQ=255)
                                               aCCAGGAAGTCCCGACGGCGTCTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGa                      >  1:2282777/1‑70 (MQ=255)
                                                ccAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATg                                             <  1:2860063/46‑1 (MQ=255)
                                                   ggAAGTCCCGACGGCGTCTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTa                 <  1:1352457/71‑1 (MQ=255)
                                                     aaGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGAtt                        >  1:3235006/1‑62 (MQ=255)
                                                     aaGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGAtt                        >  1:3246988/1‑62 (MQ=255)
                                                     aaGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGAtt                        >  1:1400226/1‑62 (MQ=255)
                                                     aaGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGAtt                        >  1:3703427/1‑62 (MQ=255)
                                                       gTCCCGACGGCGTCTGAAAAGCCGGATGTGGGACGCATGATCACCTCGt                                   <  1:721401/49‑1 (MQ=255)
                                                        tCCCGACGGCGTCTGAAAAGCCGGATGTGGGACGCGTGATCACCTCGTTGGTGCTGATTGa                      <  1:3476248/61‑1 (MQ=255)
                                                        tCCCGACGGCGTCTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGa                      <  1:1751611/61‑1 (MQ=255)
                                                          ccGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCt          >  1:1242572/1‑71 (MQ=255)
                                                          ccGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCt          >  1:3917772/1‑71 (MQ=255)
                                                          ccGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCt          >  1:2469875/1‑71 (MQ=255)
                                                          ccGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCt          <  1:3304178/71‑1 (MQ=255)
                                                          ccGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCt          <  1:1474603/71‑1 (MQ=255)
                                                          ccGACGGCGTCTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCt          <  1:504905/71‑1 (MQ=255)
                                                          ccGACGGCGTCTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCt          <  1:1573936/71‑1 (MQ=255)
                                                          ccGACGGCGTCTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCt          <  1:3232242/71‑1 (MQ=255)
                                                           cGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCTg         <  1:4014384/71‑1 (MQ=255)
                                                           cGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCTg         <  1:2947575/71‑1 (MQ=255)
                                                           cGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCTg         <  1:2069193/71‑1 (MQ=255)
                                                               ggCGTCTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCt          >  1:2608487/1‑66 (MQ=255)
                                                               ggCGTCTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCt          >  1:3152727/1‑66 (MQ=255)
                                                               ggCGTCTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCt          >  1:939143/1‑66 (MQ=255)
                                                                gCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCTGATTGc    <  1:2992177/71‑1 (MQ=255)
                                                                gCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCTGATTGc    <  1:2952704/71‑1 (MQ=255)
                                                                gCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCTGATTGc    <  1:3046490/71‑1 (MQ=255)
                                                                gCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCTGATTGc    <  1:3780556/71‑1 (MQ=255)
                                                                gCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCTGATTGc    <  1:1335971/71‑1 (MQ=255)
                                                                  gTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTACCGCGCTGATTGCTa  <  1:3849615/71‑1 (MQ=255)
                                                                  gTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTACCGCGCTGATTGCTa  <  1:3844677/71‑1 (MQ=255)
                                                                    ttGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCTGa        >  1:36561/1‑63 (MQ=255)
                                                                    |                                                                    
GCGCTATCTGGTGAAACACTCCACCACGCCGAACGGTATTCCGGATGACCAGGAAGTCCCGACGGCGTTTGAAAAGCCGGATGTGGGACGCATGATCACCTCGTTGGTGCTGATTGAAACTATCGCGCTGATTGCTA  >  minE/2513348‑2513484

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