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 2,595,752 A→G 14.6% I282I (ATT→ATC)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,7520AG14.6% 183.4 / 20.0 75I282I (ATT→ATC) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base A (31/33);  new base G (8/3);  total (39/36)
Fisher's exact test for biased strand distribution p-value = 1.95e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AAGATATTCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAAAT  >  minE/2595683‑2595821
                                                                     |                                                                     
aaGATATTCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACaa                                                                      <  1:406610/71‑1 (MQ=255)
aaGATATTCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACaa                                                                      <  1:34104/71‑1 (MQ=255)
aaGATATTCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACaa                                                                      >  1:449962/1‑71 (MQ=255)
aaGATATTCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACaa                                                                      <  1:582541/71‑1 (MQ=255)
aaGATATTCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACaa                                                                      <  1:1708659/71‑1 (MQ=255)
 aGATATTCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAAt                                                                     <  1:3340653/71‑1 (MQ=255)
 aGATATTCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAAt                                                                     <  1:1266934/71‑1 (MQ=255)
 aGATATTCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAAt                                                                     <  1:3062096/71‑1 (MQ=255)
 aGATATTCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGAGAGAAGATGACAAt                                                                     >  1:1714121/1‑71 (MQ=255)
    tatTCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCt                                                                   <  1:3226815/70‑1 (MQ=255)
    tactCCGTGAACCCTGCATTGCGCAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTg                                                                  >  1:2525585/4‑71 (MQ=255)
    tactCCGTGAACCCTGCATTGCGCAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTg                                                                  >  1:1357401/4‑71 (MQ=255)
      ttCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGcc                                                                <  1:2541932/71‑1 (MQ=255)
      ttCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGc                                                                 <  1:1969698/70‑1 (MQ=255)
         cGTGAACCCTGCATTGCGCAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCatg                                                             >  1:3096342/1‑69 (MQ=255)
         cGTGAACCCTGCATTGCGCAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCa                                                               <  1:551761/69‑1 (MQ=255)
          gTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAggg                                                            <  1:3734046/71‑1 (MQ=255)
          gTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAg                                                              <  1:405584/69‑1 (MQ=255)
            tAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAggggg                                                          >  1:472871/1‑71 (MQ=255)
            tAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAggggg                                                          >  1:2311898/1‑71 (MQ=255)
            tAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAgggg                                                           >  1:1300510/1‑70 (MQ=255)
            tAATACGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAgggg                                                           >  1:1199977/1‑70 (MQ=255)
             aaTCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAggggg                                                          >  1:1630935/1‑70 (MQ=255)
             aaTCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAggggg                                                          <  1:500776/70‑1 (MQ=255)
               tCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAc                                                       <  1:3048356/71‑1 (MQ=255)
                 cGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCAcc                                                      <  1:2819862/70‑1 (MQ=255)
                  ggCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACcgc                                                    >  1:548508/1‑71 (MQ=255)
                  ggCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACcgc                                                    >  1:2607462/1‑71 (MQ=255)
                  ggCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACcgc                                                    <  1:551492/71‑1 (MQ=255)
                    cATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGc                                                                 <  1:1164393/56‑1 (MQ=255)
                        gcgcAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGAt                                                                     >  1:353962/1‑48 (MQ=255)
                        gcgcAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGAt                                                                     >  1:2624037/1‑48 (MQ=255)
                        gcgcAGGCCATAGACCACGATGTACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAgg                                               <  1:3652944/70‑1 (MQ=255)
                          gcAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAgg                                                             <  1:1644523/54‑1 (MQ=255)
                          gcAGGCCATAAACCACCAGATAAATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACt                                            <  1:2089511/71‑1 (MQ=255)
                           cAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACtt                                           >  1:1379005/1‑71 (MQ=255)
                            aGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACttt                                          <  1:3576747/71‑1 (MQ=255)
                            aGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTCCCAGGGGGCACCGCGCAGGACttt                                          <  1:3056390/71‑1 (MQ=255)
                              gCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACaa                                                                      <  1:2817311/41‑1 (MQ=255)
                                cATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTAccc                                      <  1:3393576/71‑1 (MQ=255)
                                  tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCg                                     >  1:2769848/1‑70 (MQ=255)
                                  tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCg                                     >  1:3753967/1‑70 (MQ=255)
                                  tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCg                                     >  1:3751767/1‑70 (MQ=255)
                                  tAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCg                                     >  1:3745906/1‑70 (MQ=255)
                                   aaaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTa                                   >  1:1123326/1‑71 (MQ=255)
                                   aaaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTa                                   >  1:3490036/1‑71 (MQ=255)
                                    aaCCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAg                                                              >  1:2332685/1‑43 (MQ=255)
                                     accaccAGATACATGCCGAGCGAGAAGATGACAATCTGcc                                                                >  1:1237171/1‑40 (MQ=255)
                                      ccaccaGATACATGCCGAGCGAGAAGATGACAATCTGCCa                                                               >  1:1073704/1‑40 (MQ=255)
                                      ccaccaGATACATGCCGAGCGAGAAGATGACAATCTGCCa                                                               >  1:86078/1‑40 (MQ=255)
                                        accaGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTaa                               >  1:3168596/1‑70 (MQ=255)
                                          caGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCg                            >  1:44901/1‑71 (MQ=255)
                                           aGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGc                           <  1:2151999/71‑1 (MQ=255)
                                             gtACATGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGt                                    >  1:708703/2‑60 (MQ=255)
                                                 aTGCCGAGCGAGAAGATGACAATCTGCCAGGGGGc                                                         <  1:827032/35‑1 (MQ=255)
                                                 aTGCCCAGTGAGAAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGAcc                     >  1:2399177/1‑71 (MQ=255)
                                                    ccGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACcgcg                  <  1:799009/71‑1 (MQ=255)
                                                    ccGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACcgc                   <  1:1591466/70‑1 (MQ=255)
                                                      gagcgagAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGt                 <  1:3763092/70‑1 (MQ=255)
                                                       agcgagAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGttt               <  1:2215868/71‑1 (MQ=255)
                                                       agcgagAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGtt                >  1:248896/1‑70 (MQ=255)
                                                       agcgagAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGtt                >  1:293720/1‑70 (MQ=255)
                                                        gtgagaAAATAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCGAATGACCTCttttc              >  1:3911088/3‑70 (MQ=255)
                                                           agaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTa                                <  1:2783976/50‑1 (MQ=255)
                                                           agaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGcg           <  1:577750/71‑1 (MQ=255)
                                                           agaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGcg           <  1:3111723/71‑1 (MQ=255)
                                                            gaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTAc                                        >  1:3068514/1‑41 (MQ=255)
                                                            gaagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGcga          >  1:2588677/1‑71 (MQ=255)
                                                            gaaaaTAACGATCTGCCATGGCGCACCGCGCAGGACTTTTCCGGTGTTGATCg                            <  1:1367792/53‑1 (MQ=255)
                                                             aagaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGcgac         <  1:3075628/71‑1 (MQ=255)
                                                              agaTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGcgac         >  1:2945395/1‑70 (MQ=255)
                                                                aTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGttt               <  1:3286558/62‑1 (MQ=255)
                                                                aTGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAg             >  1:1551908/1‑64 (MQ=255)
                                                                  gACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACa     >  1:3884291/1‑70 (MQ=255)
                                                                   aCAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACaaa   >  1:3276071/1‑71 (MQ=255)
                                                                   aCAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACaaa   >  1:3030770/1‑71 (MQ=255)
                                                                    cAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAAt                              >  1:709522/1‑43 (MQ=255)
                                                                    cAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGtt                <  1:3750632/57‑1 (MQ=255)
                                                                    cAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACaaa   <  1:3873666/70‑1 (MQ=255)
                                                                    cAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAaat  <  1:1788310/71‑1 (MQ=255)
                                                                    cAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAaat  <  1:947737/71‑1 (MQ=255)
                                                                     aaTCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGt                 <  1:1194399/55‑1 (MQ=255)
                                                                     |                                                                     
AAGATATTCCGTTAATCCGGCATTGCGCAGGCCATAAACCACCAGATACATGCCGAGCGAGAAGATGACAATCTGCCAGGGGGCACCGCGCAGGACTTTACCCGTATTAATCGCATGACCGCGTTTAGCGACGACAAAT  >  minE/2595683‑2595821

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