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 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,092,381 C→T 36.2% A257T (GCC→ACC)  yhaO ← predicted transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,092,3810CT36.2% 177.3 / 170.8 163A257T (GCC→ACC) yhaOpredicted transporter
Reads supporting (aligned to +/- strand):  ref base C (52/52);  new base T (27/32);  total (79/84)
Fisher's exact test for biased strand distribution p-value = 6.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 163 total aligned reads displayed.

AATATTCTGCTCATAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGCCCGCAATGCTTTA  >  minE/2092319‑2092442
                                                              |                                                             
aaTATTCTGCTCATAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGaaa                                                        >  1:1067973/1‑70 (MQ=255)
 atatTCTGCTCATAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGaaa                                                        >  1:984575/1‑69 (MQ=255)
 atatTCTGCTCATAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGaaa                                                        >  1:2726212/1‑69 (MQ=255)
    ttCTGCTCATAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGAc                                                   <  1:3429706/71‑1 (MQ=255)
    ttCTGCTCATAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGAc                                                   <  1:2379744/71‑1 (MQ=255)
     tCTGCTCATAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGAc                                                   <  1:2923105/70‑1 (MQ=255)
      cTGCTCATAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACgg                                                 >  1:2625311/1‑71 (MQ=255)
      cTGCTCATAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGAAACGGCGTAGAAAAAGACg                                                  >  1:1019316/1‑70 (MQ=255)
            aTAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGaca                                            <  1:3758228/70‑1 (MQ=255)
            aTAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGaca                                            <  1:3627792/70‑1 (MQ=255)
            aTAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGaca                                            <  1:1673480/70‑1 (MQ=255)
                gCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGa                                                          <  1:2972034/52‑1 (MQ=255)
                gCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGacaaaca                                        >  1:880935/1‑70 (MQ=255)
                  ttttACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACaaaa                                     >  1:3649811/1‑71 (MQ=255)
                  ctttACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACaaaa                                     >  1:688535/2‑71 (MQ=255)
                    ttACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGaca                                            >  1:1969865/1‑62 (MQ=255)
                    ttACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGaca                                            >  1:2811236/1‑62 (MQ=255)
                    ttACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAAt                                    <  1:812362/70‑1 (MQ=255)
                    ttACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAAt                                    <  1:3002314/70‑1 (MQ=255)
                    ttACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATg                                   >  1:1778919/1‑71 (MQ=255)
                         gCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCaaa                              >  1:1326107/1‑71 (MQ=255)
                         gCTTCGTCATGTCCCATCGCCAGCGAGAACGACACGGCGTAg                                                           >  1:1398875/1‑42 (MQ=255)
                            aagcgggaaggaaaaagaagcaactaaacgagGGTGTAGaaaaa                                                      <  1:3162449‑M2/12‑1 (MQ=255)
                            aagcgggaaggaaaaagaagcaactaaacgagGGTGTAGaaaaa                                                      <  1:3415310‑M2/12‑1 (MQ=255)
                            aagcgggaaggaaaaagaagcaactaaacgagGGTGTAGaaaaa                                                      <  1:2546241‑M2/12‑1 (MQ=255)
                            aagcgggaaggaaaaagaagcaactaaacgagGGTGTAGaaaaa                                                      <  1:2085695‑M2/12‑1 (MQ=255)
                            aagcgggaaggaaaaagaagcaactaaacgagGGTGTAGAAAAAGAc                                                   <  1:767643‑M2/15‑1 (MQ=255)
                            aagcgggaaggaaaaagaagcaactaaacgagGGCGTAGAAAAAGa                                                    >  1:3882729‑M2/33‑46 (MQ=255)
                            aagcgggaaggaaaaagaagcaactaaacgagGGCGTAGAAAAAGa                                                    >  1:3503282‑M2/33‑46 (MQ=255)
                            aagcgggaaggaaaaagaagcaactaaacgagGGCGTAGAAAAAGa                                                    >  1:656712‑M2/33‑46 (MQ=255)
                            aagcgggaaggaaaaagaagcaactaaacgagGGCGTAGAAAAAGa                                                    >  1:2439179‑M2/33‑46 (MQ=255)
                            aagcgggaaggaaaaagaagcaactaaacgagGGCGTAGAAAAAGa                                                    >  1:2314925‑M2/33‑46 (MQ=255)
                            aagcgggaaggaaaaagaagcaactaaacgagGGCGTAGAAAAAGa                                                    >  1:1367944‑M2/33‑46 (MQ=255)
                            aagcgggaaggaaaaagaagcaactaaacgagGGCGTAGAAAAAGa                                                    >  1:1972874‑M2/33‑46 (MQ=255)
                             cGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAAcgc                           >  1:1034715/1‑70 (MQ=255)
                              gcgggaaggaaaaagaagcaactaaacgagGGTGTAGaaaaa                                                      >  1:2246439‑M2/31‑42 (MQ=255)
                              gcgggaaggaaaaagaagcaactaaacgagGGTGTAGaaaaa                                                      >  1:2402717‑M2/31‑42 (MQ=255)
                              gcgggaaggaaaaagaagcaactaaacgagGGTGTAGAAAAAg                                                     <  1:2276974‑M2/13‑1 (MQ=255)
                              gcgggaaggaaaaagaagcaactaaacgagGGTGTAGAAAAAg                                                     <  1:693249‑M2/13‑1 (MQ=255)
                              gcgggaaggaaaaagaagcaactaaacgagGGCGTa                                                            <  1:2961513‑M2/6‑1 (MQ=255)
                              gcgggaaggaaaaagaagcaactaaacgagGGCGTa                                                            <  1:2174559‑M2/6‑1 (MQ=255)
                              gcgggaaggaaaaagaagcaactaaacgagGGCGTa                                                            <  1:3269325‑M2/6‑1 (MQ=255)
                              gcgggaaggaaaaagaagcaactaaacgagGGCGTAGAAAAAGAcga                                                 >  1:3517914‑M2/31‑46 (MQ=255)
                              gcgggaaggaaaaagaagcaactaaacgagGGCGTAGAAAAAGAcga                                                 >  1:3988938‑M2/31‑46 (MQ=255)
                              gcgggaaggaaaaagaagcaactaaacgagGGCGTAGAAAAAGAcga                                                 >  1:122999‑M2/31‑46 (MQ=255)
                              gcgggaaggaaaaagaagcaactaaacgagGGCGTAGAAAAAGACg                                                  >  1:1566646‑M2/31‑46 (MQ=255)
                              gTCATGTCCCATCGCCAGCGAGAACGACACGGCGTAGaaaaa                                                      >  1:1100100/1‑42 (MQ=255)
                               tCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGa                                                    <  1:2965991/43‑1 (MQ=255)
                                gggaaggaaaaagaagcaactaaacgagGGTGTAGAAAAAGa                                                    >  1:1487338‑M2/29‑42 (MQ=255)
                                gggaaggaaaaagaagcaactaaacgagGGTGTAGAAAAAGAc                                                   >  1:1095419‑M2/29‑43 (MQ=255)
                                gggaaggaaaaagaagcaactaaacgagGGTGTAGAAAAAGAc                                                   >  1:460663‑M2/29‑43 (MQ=255)
                                gggaaggaaaaagaagcaactaaacgagGGTGTAGAAAAAGAc                                                   >  1:2900098‑M2/29‑43 (MQ=255)
                                gggaaggaaaaagaagcaactaaacgagGGTGTAGAAAAAGAc                                                   >  1:2118000‑M2/29‑43 (MQ=255)
                                 ggaaggaaaaagaagcaactaaacgagGGTGTAGaaaaa                                                      <  1:1312628‑M2/12‑1 (MQ=255)
                                 ggaaggaaaaagaagcaactaaacgagGGTGTAGaaaaa                                                      <  1:920354‑M2/12‑1 (MQ=255)
                                 ggaaggaaaaagaagcaactaaacgagGGTGTAGaaaaa                                                      <  1:4221722‑M2/12‑1 (MQ=255)
                                 ggaaggaaaaagaagcaactaaacgagGGCGTAGAAAAAGAc                                                   <  1:1289607‑M2/15‑1 (MQ=255)
                                 aTGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGatat                      >  1:2341977/1‑71 (MQ=255)
                                 aTGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGatat                      >  1:497702/1‑71 (MQ=255)
                                  gaaggaaaaagaagcaactaaacgagGGTGTAGAAAAAg                                                     <  1:2117350‑M2/13‑1 (MQ=255)
                                   aaggaaaaagaagcaactaaacgagGGTGTAGAAAAAg                                                     >  1:2070007‑M2/26‑38 (MQ=255)
                                   aaggaaaaagaagcaactaaacgagGGTGTAGAAAAAGACg                                                  >  1:3907930‑M2/26‑41 (MQ=255)
                                    tCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTc                    <  1:3932777/70‑1 (MQ=255)
                                    tCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTc                    <  1:4193956/70‑1 (MQ=255)
                                    aggaaaaagaagcaactaaacgagGGTGTAGAAAAAGAcga                                                 <  1:3736238‑M2/17‑2 (MQ=255)
                                    aggaaaaagaagcaactaaacgagGGTGTAGAAAAAGAcga                                                 <  1:833632‑M2/17‑2 (MQ=255)
                                    aggaaaaagaagcaactaaacgagGGTGTAGAAAAAGACg                                                  <  1:1873114‑M2/16‑1 (MQ=255)
                                    aggaaaaagaagcaactaaacgagGGCGTAGAAAAAGACg                                                  <  1:3039673‑M2/16‑1 (MQ=255)
                                     ggaaaaagaagcaactaaacgagGGTGTAGAAAAAGAcga                                                 <  1:2021355‑M2/17‑2 (MQ=255)
                                     ggaaaaagaagcaactaaacgagGGTGTAGAAAAAGAcga                                                 <  1:1696351‑M2/17‑2 (MQ=255)
                                     cccATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTc                    <  1:3384701/69‑1 (MQ=255)
                                       aaaaagaagcaactaaacgagGGTGTAGAAAAAGa                                                    >  1:2749850‑M2/22‑35 (MQ=255)
                                       aaaaagaagcaactaaacgagGGTGTAGAAAAAGAc                                                   >  1:2738424‑M2/22‑36 (MQ=255)
                                        aaaagaagcaactaaacgagGGTGTAGAAAAAGAc                                                   >  1:101259‑M2/21‑35 (MQ=255)
                                        aaaagaagcaactaaacgagGGTGTAGAAAAAGAc                                                   >  1:2686219‑M2/21‑35 (MQ=255)
                                        aaaagaagcaactaaacgagGGTGTAGAAAAAGAc                                                   >  1:2858928‑M2/21‑35 (MQ=255)
                                           gCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGc               >  1:1043364/1‑68 (MQ=255)
                                           gCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGc               >  1:3582678/1‑68 (MQ=255)
                                           gCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGc               >  1:3263789/1‑68 (MQ=255)
                                             cAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGCCCGc           <  1:1705446/70‑1 (MQ=255)
                                             cAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGCCCGc           <  1:1742710/70‑1 (MQ=255)
                                              aGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCTATATTCATTGCCCGCaa         <  1:2191042/71‑1 (MQ=255)
                                                 gTGAACGACACTGCGTAGAAAAAGACGGTGACAAACaaaa                                     >  1:1303074/1‑40 (MQ=255)
                                                 gTGAACGACACGGCGTAGAAAAAGACTGTGACAAACAAAATGCCAAACGCGATAtt                     >  1:2691563/1‑56 (MQ=255)
                                                 gTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATAtt                     >  1:262477/1‑56 (MQ=255)
                                                  tGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGa                         <  1:46451/51‑1 (MQ=255)
                                                  tGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATAtt                     <  1:2471867/55‑1 (MQ=255)
                                                  tGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATAtt                     <  1:1823043/55‑1 (MQ=255)
                                                   gAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGCCCGCAATGCtt    >  1:3816437/1‑71 (MQ=255)
                                                    aaCGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGCCCGCAATGCttt   <  1:805827/71‑1 (MQ=255)
                                                    aaCGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGCCCGCAATGCtt    <  1:3530302/70‑1 (MQ=255)
                                                    aaCGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGCCCGCAATGCtt    <  1:3761894/70‑1 (MQ=255)
                                                     aCGACACGGCGTAGAAAAAGACGGTGACAAACAAAATg                                   >  1:4255381/1‑38 (MQ=255)
                                                     aCGACACGGCGTAGAAAAAGACGGTGACAAACAAAATg                                   >  1:3647773/1‑38 (MQ=255)
                                                     aCGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGCCCGCAATGCttt   <  1:2538525/70‑1 (MQ=255)
                                                     aCGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGCCCGCAATGCTTTa  >  1:641751/1‑71 (MQ=255)
                                                        acacGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAATCGCGa                         <  1:1915316/45‑1 (MQ=255)
                                                        acacGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGa                         <  1:2934472/45‑1 (MQ=255)
                                                        acacGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGa                         <  1:288277/45‑1 (MQ=255)
                                                           cGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGc               <  1:3894418/52‑1 (MQ=255)
                                                              |                                                             
AATATTCTGCTCATAGGCTTTTACCGCTTCGTCATGTCCCATCGCCAGCGTGAACGACACGGCGTAGAAAAAGACGGTGACAAACAAAATGCCAAACGCGATATTCATTGCCCGCAATGCTTTA  >  minE/2092319‑2092442

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A