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 2,094,003 C→A 21.7% T283T (ACG→ACT)  tdcG ← L‑serine dehydratase 3

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,094,0030CA21.7% 178.1 / 26.6 74T283T (ACG→ACT) tdcGL‑serine dehydratase 3
Reads supporting (aligned to +/- strand):  ref base C (31/26);  new base A (8/8);  total (40/34)
Fisher's exact test for biased strand distribution p-value = 7.84e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGGACGACGGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACATGTTGATCCAGTCGAT  >  minE/2093933‑2094071
                                                                      |                                                                    
ccGGACGACGGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGcc                                                                      <  1:1854728/71‑1 (MQ=255)
ccGGACGACGGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGcc                                                                      <  1:3129887/71‑1 (MQ=255)
 cGGACGACGGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCg                                                                     <  1:1144772/71‑1 (MQ=255)
 cGGACGACGGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCg                                                                     >  1:893794/1‑71 (MQ=255)
 cGGACGACGGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCg                                                                     >  1:2878945/1‑71 (MQ=255)
 cGGACGACGGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCg                                                                     >  1:3357418/1‑71 (MQ=255)
  ggACGACGGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGt                                                                    <  1:989600/71‑1 (MQ=255)
   gacgacGGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGt                                                                    >  1:409085/1‑70 (MQ=255)
   gacgacGGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGt                                                                    >  1:3551870/1‑70 (MQ=255)
     cgacgGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTAc                                                                 <  1:1173665/71‑1 (MQ=255)
     cgacgGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTAc                                                                 <  1:3261656/71‑1 (MQ=255)
      gacgGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTa                                                                  <  1:3471859/69‑1 (MQ=255)
      gacgGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTAcc                                                                <  1:1039982/71‑1 (MQ=255)
      gacgGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTAcc                                                                <  1:3532993/71‑1 (MQ=255)
      gacgGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTAcc                                                                <  1:84647/71‑1 (MQ=255)
         taaaCTTGTCGTAGTACGCCAGAACTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTcaccac                                                              <  1:711265/68‑1 (MQ=255)
          gAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCAcgc                                                            <  1:186443/71‑1 (MQ=255)
           aaCTTGTCGTAGTACGCCAGAACTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCAcgc                                                            <  1:163734/70‑1 (MQ=255)
           aaCTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCAcgcg                                                           >  1:279286/1‑71 (MQ=255)
           aaCTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCAcgcg                                                           >  1:99484/1‑71 (MQ=255)
             cTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACgcgc                                                          >  1:389199/1‑70 (MQ=255)
             cTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGcgcc                                                         >  1:2520396/1‑71 (MQ=255)
             cTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGcgcc                                                         >  1:2515975/1‑71 (MQ=255)
              ttATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCAcg                                                             <  1:3082986/66‑1 (MQ=255)
               tgtCGTAGTACGCCAGAACTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCACGcgaccg                                                       >  1:3615862/3‑71 (MQ=255)
               tgtCGTAGTACGCCAGAACTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCACGcgacc                                                        >  1:3278248/3‑70 (MQ=255)
                aTCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGcgcccgc                                                      >  1:1591342/1‑71 (MQ=255)
                aTCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGcgcccgc                                                      >  1:1539540/1‑71 (MQ=255)
                aTCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGcgcccgc                                                      >  1:1624712/1‑71 (MQ=255)
                aTCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGcgcccgc                                                      >  1:73143/1‑71 (MQ=255)
                 tCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGcgcccgcc                                                     <  1:2693478/71‑1 (MQ=255)
                 tCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGcgcccgc                                                      <  1:2267458/70‑1 (MQ=255)
                  cGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGcgcccgc                                                      >  1:1069282/1‑69 (MQ=255)
                  cGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGcgcccgc                                                      >  1:3070272/1‑69 (MQ=255)
                   gTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTa                                                                  >  1:1458611/1‑56 (MQ=255)
                   gTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAg                                                   <  1:885111/71‑1 (MQ=255)
                   gTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAg                                                   >  1:2664009/1‑71 (MQ=255)
                    taataaGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGc                                                  >  1:2931244/1‑71 (MQ=255)
                     aataaGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGcgccc                                                        >  1:103838/1‑64 (MQ=255)
                         cgCCAGAACTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCACGCGACCGCCAGCAGCGt                                             <  1:878775/70‑1 (MQ=255)
                          gCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGtt                                            <  1:3639644/71‑1 (MQ=255)
                          gCCAGAACTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCTCAGTCACCACGCGACCGCCAGCAGCGtt                                            <  1:1300937/71‑1 (MQ=255)
                           ccAGAACTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCACGCGACCGCCAGCAGCGttc                                           <  1:344529/71‑2 (MQ=255)
                            cAGAACTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCAcgcgac                                                         >  1:1228213/1‑54 (MQ=255)
                            cAGAACTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCACGCGACCGCCAGCAGCGttct                                          >  1:3765492/1‑69 (MQ=255)
                              gaaCTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCACGCGACCGCCAg                                                   >  1:636282/3‑60 (MQ=255)
                              gTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTttct                                        >  1:2667918/1‑71 (MQ=255)
                              gTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTttct                                        >  1:3707312/1‑71 (MQ=255)
                               tACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTttctt                                       <  1:3127909/71‑1 (MQ=255)
                               aaCTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCACGCGACCGCCAGCAGCGTTctctt                                       >  1:3484239/2‑71 (MQ=255)
                                aCTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCACGcgacc                                                        >  1:3847039/1‑53 (MQ=255)
                                 cTGCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCACGCGACCGCCAGCAGCGTTctcttcg                                     <  1:1568880/71‑2 (MQ=255)
                                 cTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTttcttc                                      >  1:1453895/1‑70 (MQ=255)
                                   gCCGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCACGCGACCGCCAGCAGCGTtctc                                         <  1:346085/65‑1 (MQ=255)
                                   gCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTttctt                                       >  1:1656806/1‑67 (MQ=255)
                                    ccGGGATAATCCCGCACGCACCGTTAGTCGGCGCAGTCACCACGCGACCGCCAGCAGCGtt                                            >  1:986529/1‑61 (MQ=255)
                                     cGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTaa                                 <  1:2554477/71‑1 (MQ=255)
                                     cGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTaa                                 <  1:421292/71‑1 (MQ=255)
                                      ggAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAAc                                >  1:3107302/1‑71 (MQ=255)
                                         ataatGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGcgcccgcc                                                     >  1:3078741/1‑47 (MQ=255)
                                              gCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGc                             <  1:1832254/66‑1 (MQ=255)
                                                 gcacgcacCGTTAGTCGGTGCGGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGcgcg                      >  1:777986/1‑70 (MQ=255)
                                                 gcacgcacCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAgcgc                       >  1:1339390/1‑69 (MQ=255)
                                                  cacgcacCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGt                     >  1:2436712/1‑70 (MQ=255)
                                                     gcacCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGc                             <  1:1597629/59‑1 (MQ=255)
                                                     gcacCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAgcg                        <  1:1285285/64‑1 (MQ=255)
                                                     gcacCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACAt                 >  1:1447402/1‑71 (MQ=255)
                                                      cacCGTTAGTCGGCGCAGTCACCACGCGACCGCCAGCAGCGTTCTCTTCGTTCACTGCCAGTGCAAACATg                <  1:1704461/71‑1 (MQ=255)
                                                         cGTTAGTCGGTGCCGTGACCACGCGCCCGCCAGCTGCGTTttct                                        >  1:56041/1‑44 (MQ=255)
                                                          gTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACt                                   <  1:1731682/48‑1 (MQ=255)
                                                          gTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCTCCAGCGCGTACATGTTGa            <  1:3195049/71‑1 (MQ=255)
                                                            tAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACATGTTGATc          >  1:3610100/1‑71 (MQ=255)
                                                             aGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACATGTTGATc          <  1:2531017/70‑1 (MQ=255)
                                                             aGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACATGTTGATc          <  1:745603/70‑1 (MQ=255)
                                                              gTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACATGTTGATCCa        <  1:1597341/71‑1 (MQ=255)
                                                               tCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACATGtt              <  1:844842/64‑1 (MQ=255)
                                                                     ccGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACATGTTGATCCAGTCGAt  <  1:2473296/70‑1 (MQ=255)
                                                                     ccGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACATGTTGATCCAGTCGAt  <  1:1377253/70‑1 (MQ=255)
                                                                     ccGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACATGTTGATCCAGTCGAt  >  1:291964/1‑70 (MQ=255)
                                                                      cGTTACGACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACATGTTGAt           >  1:3359/1‑60 (MQ=255)
                                                                      cGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACATGTTGAt           >  1:1839150/1‑60 (MQ=255)
                                                                      |                                                                    
CCGGACGACGGAACTTATCGTAATAAGCCAGTACTGCCGGAATAATGCCGCACGCACCGTTAGTCGGTGCCGTTACCACGCGCCCGCCAGCTGCGTTTTCTTCACTAACCGCCAGCGCGTACATGTTGATCCAGTCGAT  >  minE/2093933‑2094071

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