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
A5 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,533,883 T→C 36.6% intergenic (‑24/+125) yiiM ← / ← kdgT conserved hypothetical protein/2‑keto‑3‑deoxy‑D‑gluconate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,533,8830TC36.6% 85.9 / 95.3 93intergenic (‑24/+125)yiiM/kdgTconserved hypothetical protein/2‑keto‑3‑deoxy‑D‑gluconate transporter
Reads supporting (aligned to +/- strand):  ref base T (28/30);  new base C (15/18);  total (44/49)
Fisher's exact test for biased strand distribution p-value = 8.30e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATAAGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCCAGGCAGGAACTCAA  >  W3110S.gb/3533815‑3533953
                                                                    |                                                                      
aTAAGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTcc                                                                      >  1:1693142/1‑71 (MQ=255)
aTAAGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTcc                                                                      <  1:1194245/71‑1 (MQ=255)
aTAAGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTcc                                                                      >  1:1512979/1‑71 (MQ=255)
 tAAGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTccc                                                                     <  1:1279623/71‑1 (MQ=255)
    gCCTGAATCTTGGCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCAt                                                                  <  1:1927902/71‑1 (MQ=255)
    gCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCGTCTCCACGAGAAATTCCCCCAt                                                                  <  1:744791/71‑1 (MQ=255)
       tGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCAt                                                                  <  1:4698390/68‑1 (MQ=255)
        gAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGa                                                              >  1:4276226/1‑71 (MQ=255)
         aaTCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTa                                                                <  1:2790918/68‑1 (MQ=255)
         aaTCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGa                                                              <  1:3060628/70‑1 (MQ=255)
         aaTCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGAc                                                             >  1:4347357/1‑71 (MQ=255)
            cTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCa                                                           >  1:586986/1‑70 (MQ=255)
               gCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCAtatt                                                       >  1:1795656/1‑71 (MQ=255)
               gCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCata                                                         <  1:2216013/69‑1 (MQ=255)
                    tgtATACGTCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTa                                                                >  1:3925134/1‑57 (MQ=255)
                    tgtATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATatttattt                                                  <  1:2564705/71‑1 (MQ=255)
                    tgtATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTa                                                                >  1:4053947/1‑57 (MQ=255)
                      tataCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATatttattt                                                  <  1:940099/69‑1 (MQ=255)
                      tataCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATAtttatttt                                                 <  1:4078231/70‑1 (MQ=255)
                      tataCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATAtttatttt                                                 <  1:1270645/70‑1 (MQ=255)
                      tataCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTACCCCATTAGACCATAtttatttt                                                 >  1:1992415/1‑70 (MQ=255)
                      tataCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATT‑‑CCCATTAGACCATAtttatttt                                                 <  1:2336053/68‑1 (MQ=255)
                        taCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTccc                                                                     >  1:3069847/1‑48 (MQ=255)
                        taCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATAtttattttat                                               <  1:1131875/70‑1 (MQ=255)
                        taCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATg                                              >  1:4824213/1‑71 (MQ=255)
                        taCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATg                                              >  1:3913287/1‑71 (MQ=255)
                         aCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCAtattta                                                     >  1:2071044/1‑63 (MQ=255)
                         aCATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGt                                             >  1:767692/1‑71 (MQ=255)
                          cATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGt                                             >  1:4682804/1‑70 (MQ=255)
                          cATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGt                                             <  1:3278920/70‑1 (MQ=255)
                           aTCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTa                                                                >  1:1861918/1‑50 (MQ=255)
                           aTCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTa                                                                >  1:3359300/1‑50 (MQ=255)
                            tCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTa                                                                <  1:2754657/49‑1 (MQ=255)
                            tCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTa                                                                <  1:3314368/49‑1 (MQ=255)
                            tCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAg                                          <  1:1835205/71‑1 (MQ=255)
                              aaCCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAg                                          >  1:325496/1‑69 (MQ=255)
                              aaCCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGc                                        >  1:32391/1‑71 (MQ=255)
                              aaCCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTa                                                                >  1:3175869/1‑47 (MQ=255)
                                ccGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGt                                      <  1:1130745/71‑1 (MQ=255)
                                    atatCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTg                                  <  1:3535960/71‑1 (MQ=255)
                                    atatCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTg                                  <  1:2788296/71‑1 (MQ=255)
                                     tatCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTg                                  <  1:3363138/70‑1 (MQ=255)
                                       tCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGttt                               <  1:778332/71‑1 (MQ=255)
                                       tCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGttt                               <  1:2043733/71‑1 (MQ=255)
                                       tCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTa                                                                >  1:1629274/1‑38 (MQ=255)
                                       tCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTa                                                                >  1:2728748/1‑38 (MQ=255)
                                       tCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGtt                                <  1:305869/70‑1 (MQ=255)
                                       tCGCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGtt                                <  1:2058122/70‑1 (MQ=255)
                                         gCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTc                             >  1:1132100/1‑71 (MQ=255)
                                         gCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTc                             >  1:3961633/1‑71 (MQ=255)
                                         gCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTc                             >  1:929133/1‑71 (MQ=255)
                                         gCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTc                             <  1:4097292/71‑1 (MQ=255)
                                         gCATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTc                             <  1:4351751/71‑1 (MQ=255)
                                          cATCTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTcg                            >  1:5100962/1‑71 (MQ=255)
                                            tCTGTTCCCTCTCAACGAGAAATTTCCCCATTAGACCATATTTATTTTATGt                                             <  1:5029877/52‑1 (MQ=255)
                                             cTGTTCCCTCTCCACGAGAAATTCCCCCATTAGACCATAtttatttt                                                 <  1:4635763/47‑1 (MQ=255)
                                              tGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCAtatttatt                                                   >  1:2919854/1‑44 (MQ=255)
                                              tGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATAtttatttta                                                >  1:1391407/1‑47 (MQ=255)
                                              tGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATAtttatttta                                                >  1:2705876/1‑47 (MQ=255)
                                              tGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATAtttatttta                                                >  1:1397439/1‑47 (MQ=255)
                                               gTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGt                                             <  1:4110133/49‑1 (MQ=255)
                                                ttCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCgg                         <  1:713618/68‑1 (MQ=255)
                                                ttCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGt                        <  1:809350/69‑1 (MQ=255)
                                                ttCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTcgcg                          <  1:1363424/67‑1 (MQ=255)
                                                ttCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTcgcg                          <  1:4655275/67‑1 (MQ=255)
                                                ttCCCTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTaa                      <  1:337683/71‑1 (MQ=255)
                                                  cccTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAg                     >  1:2005532/1‑70 (MQ=255)
                                                  cccTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTaa                      <  1:331549/69‑1 (MQ=255)
                                                  cccTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAg                     >  1:1128570/1‑70 (MQ=255)
                                                  cccTCTCCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAg                     <  1:606816/70‑1 (MQ=255)
                                                      ctcCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAg                                          >  1:2083745/1‑45 (MQ=255)
                                                       tcCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATc                 >  1:1093383/1‑69 (MQ=255)
                                                       tcCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATc                 <  1:3095668/69‑1 (MQ=255)
                                                       tcCACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATc                 >  1:3332224/1‑69 (MQ=255)
                                                        ccACGAGAAATTCCCCCATTAGACCATatttattt                                                  <  1:2935680/35‑1 (MQ=255)
                                                         cACGAGAAATTTCCCCATTAGACCATAtttatttt                                                 >  1:1875900/1‑35 (MQ=255)
                                                         cACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCcagg             >  1:4727637/1‑71 (MQ=255)
                                                         cACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGt                                 >  1:3475161/1‑51 (MQ=255)
                                                         cACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGt                                 >  1:4708286/1‑51 (MQ=255)
                                                         cACGAGAAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGt                                 >  1:271139/1‑51 (MQ=255)
                                                          aCGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGtt                                <  1:4322498/51‑1 (MQ=255)
                                                           cGAGAAATTTCCCCATTAGACCATAtttattttat                                               <  1:519885/35‑1 (MQ=255)
                                                           cGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCa                                           >  1:2710317/1‑39 (MQ=255)
                                                            gagaAATTTCCCCATTAGACCATATTTATTTTATGTCAgg                                         >  1:941664/1‑40 (MQ=255)
                                                            gagaAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGt                                      <  1:3301835/43‑1 (MQ=255)
                                                            gagaAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCcaggcag          <  1:4135869/71‑1 (MQ=255)
                                                              gaAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGtttt                              <  1:76700/49‑1 (MQ=255)
                                                              gaAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGtttt                              <  1:1482613/49‑1 (MQ=255)
                                                              gaAATTCCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCCAGGCAGGa        <  1:3597748/71‑1 (MQ=255)
                                                               aaaTTTCCCCATTAGACCATATTTATTTTATGTCa                                           >  1:2404544/1‑35 (MQ=255)
                                                               aaaTTTCCCCATTAGACCATATTTATTTTATGTCa                                           >  1:1323318/1‑35 (MQ=255)
                                                                 aTTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGt                    <  1:2923171/56‑1 (MQ=255)
                                                                 aTTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCcaggca           <  1:3083298/65‑1 (MQ=255)
                                                                  tttCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCCAGGCAGGAACTc    <  1:1674921/71‑1 (MQ=255)
                                                                    tCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCCAGGCAGGAACTCaa  >  1:4178394/1‑71 (MQ=255)
                                                                    |                                                                      
ATAAGCCTGAATCTTGCCTGTGTATACATCAACCGGATATCGCATCTGTTCCCTCTCCACGAGAAATTTCCCCATTAGACCATATTTATTTTATGTCAGGCGTGCTGTTTTCGCGGTAAGTATCCAGGCAGGAACTCAA  >  W3110S.gb/3533815‑3533953

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