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 F1 I0 R2 230 93.6 4701257 96.3% 4527310 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,266,955 T→C 46.2% E151G (GAA→GGA)  yecA ← conserved metal‑binding protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,266,9550TC46.2% 11.0 / 103.9 78E151G (GAA→GGA) yecAconserved metal‑binding protein
Reads supporting (aligned to +/- strand):  ref base T (20/22);  new base C (14/22);  total (34/44)
Fisher's exact test for biased strand distribution p-value = 4.97e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.90e-01

CCAGTCGAATGGCATCTACGCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACGTTGACCAGT  >  minE/1266887‑1267021
                                                                    |                                                                  
ccAGTCGAATGGCATCTACGCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTcc                                                                  >  1:213119/1‑71 (MQ=255)
  aGTCGAATGGCATCTACGCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTCCCTc                                                                <  1:1833983/71‑1 (MQ=255)
    tCGAATGGCATCTACGCTCTCTTCAAACGCTTCTGGCTACATCTTTTCTACCCGCTCGAAGTTTCCCTc                                                                <  1:1692001/69‑1 (MQ=255)
      gAATGGCATCTACGCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTa                                                            >  1:1681569/1‑71 (MQ=255)
      gAATGGCATCTACGCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTCCCTCAGTa                                                            >  1:2507898/1‑71 (MQ=255)
      gAATGGCATCTACGCTCTCTTCAAACGCTTATGGCGACATCTTTTCTACCCGCTCGAAGTTTCCCTCAGTa                                                            >  1:3577103/1‑71 (MQ=255)
       aaTGGCATCTACGCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTAACCGCTCGAAGTTTTCCTCAGTa                                                            <  1:624349/70‑1 (MQ=255)
         tGGCATCTACGCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCg                                                         <  1:2722254/71‑1 (MQ=255)
         tGGCATCTACGCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTCCCTCAGTACCg                                                         <  1:3016698/71‑1 (MQ=255)
           gCATCTACGCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTg                                                       <  1:4270572/71‑1 (MQ=255)
           gCATCTACGCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTg                                                       >  1:1534242/1‑71 (MQ=255)
                tACGCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTCCCTCa                                                               >  1:4132345/1‑58 (MQ=255)
                  cGCTCTCTTCAAACTCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAg                                                    <  1:2815013/67‑1 (MQ=255)
                   gCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCaa                                               <  1:4507166/71‑1 (MQ=255)
                       tctTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATc                                             <  1:2783428/69‑1 (MQ=255)
                       tctTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAATc                                             <  1:2515622/69‑1 (MQ=255)
                       tctTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAATc                                             <  1:1166101/69‑1 (MQ=255)
                        ctTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCa                                                     >  1:2321098/1‑60 (MQ=255)
                         ttCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCt                                         >  1:3672578/1‑71 (MQ=255)
                         ttCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTCACTCAGTACCGTGCAGCGCaa                                               >  1:1624467/1‑65 (MQ=255)
                           cAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTc                                        <  1:4052398/70‑1 (MQ=255)
                           cAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTCCCTCAg                                                              >  1:2700578/1‑48 (MQ=255)
                           cAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTc                                        <  1:4332699/70‑1 (MQ=255)
                            aaaCGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTcc                                       <  1:960689/70‑1 (MQ=255)
                            aaaCGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTcc                                       <  1:3386258/70‑1 (MQ=255)
                            aaaCGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTCCCTc                                                                <  1:2320577/45‑1 (MQ=255)
                             aaCGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTccc                                                                  >  1:1744969/1‑42 (MQ=255)
                              aCGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCa                                                <  1:1793680/59‑1 (MQ=255)
                               cGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAgcg                                   >  1:3734278/1‑71 (MQ=255)
                               cGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTCCCTCa                                                               >  1:2888662/1‑43 (MQ=255)
                               cGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAgcg                                   <  1:3728171/71‑1 (MQ=255)
                                gCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAgcgc                                  >  1:1032961/1‑71 (MQ=255)
                                 cTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCt                                 >  1:1506488/1‑71 (MQ=255)
                                  ttCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTg                                >  1:3929480/1‑71 (MQ=255)
                                    cTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTg                                <  1:3312356/69‑1 (MQ=255)
                                     tGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGt                                                        <  1:3031944/44‑1 (MQ=255)
                                      ggCGACATCTTTTCTACCCGCTCGAAGTTTCCCTCAGTACCGTGc                                                      <  1:2433521/45‑1 (MQ=255)
                                      ggCGACATCTTTTCTACCCGCTCGAAGTTTCCCTCAGTACCGTGc                                                      <  1:4392014/45‑1 (MQ=255)
                                       gCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGtt                             <  1:4396188/69‑1 (MQ=255)
                                       gCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGt                              <  1:994662/68‑1 (MQ=255)
                                        cGACATCTTTTCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGtttt                           >  1:4631213/1‑70 (MQ=255)
                                         gACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTaa                         <  1:2665451/71‑1 (MQ=255)
                                           cATCTTTTCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAAt                                              >  1:4626276/1‑48 (MQ=255)
                                            aTCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCaa                                               >  1:348555/1‑46 (MQ=255)
                                            aTCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGa                      <  1:2456398/71‑1 (MQ=255)
                                             tCTTTTCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCa                                                <  1:1323083/44‑1 (MQ=255)
                                              cTTTTCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAgcgc                                                 <  1:2184033/42‑1 (MQ=255)
                                               ttttCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTaa                         >  1:4224901/1‑65 (MQ=255)
                                               ttttCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGa                      <  1:1529109/68‑1 (MQ=255)
                                               ttttCTACCCGCTCGAAGTTTCCCTCAGAACCGTGc                                                      >  1:252705/1‑36 (MQ=38)
                                                tttCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAgc                                    <  1:573801/53‑1 (MQ=255)
                                                 ttCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCgg                 >  1:3919484/1‑71 (MQ=255)
                                                 ttCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCgg                 >  1:3013056/1‑71 (MQ=255)
                                                 ttCTACCCGCTCGAAGTTTCCCTCAGTTCCGTGCAGCGCAATCGCCTCCAGCGCTGGtttt                           <  1:2103441/61‑1 (MQ=255)
                                                 ttCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGaa                     <  1:2267602/67‑1 (MQ=255)
                                                 ttCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGaa                     <  1:3355284/67‑1 (MQ=255)
                                                 ttCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGaa                     <  1:2857452/67‑1 (MQ=255)
                                                 ttCTACCCGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCgg                 >  1:2682462/1‑71 (MQ=255)
                                                      cccGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAAc            <  1:2263027/71‑1 (MQ=255)
                                                       ccGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACg           <  1:1198140/71‑1 (MQ=255)
                                                       ccGCTCGAAGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACg           <  1:124726/71‑1 (MQ=255)
                                                         gCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACGtt         >  1:1356164/1‑71 (MQ=255)
                                                         gCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACGtt         <  1:2784948/71‑1 (MQ=255)
                                                          cTCGAAGTTTCCCTCACTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACGTTg        <  1:4292016/71‑1 (MQ=255)
                                                           tCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAg                                     >  1:1983153/1‑41 (MQ=255)
                                                           tCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAg                                     >  1:3085914/1‑41 (MQ=255)
                                                            cGAAGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGaa                     >  1:663661/1‑56 (MQ=255)
                                                             gAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTTGTTTTAACGAATCGGGCAACGTTGAcc     <  1:1409400/71‑1 (MQ=255)
                                                             gAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACGTTGAc      >  1:1945148/1‑70 (MQ=255)
                                                             gAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACGTTGAc      >  1:3565639/1‑70 (MQ=255)
                                                              aaGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACGTTGAc      <  1:3686034/69‑1 (MQ=255)
                                                              aaGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACGTTGAc      <  1:425726/69‑1 (MQ=255)
                                                               aGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGaa                     >  1:4505891/1‑53 (MQ=255)
                                                               aGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAAt                    >  1:3549108/1‑54 (MQ=255)
                                                               aGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAAt                    >  1:754144/1‑54 (MQ=255)
                                                               aGTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACGTTGACCAg   <  1:4318554/71‑1 (MQ=255)
                                                                gTTTTCCTCAGTACCGTGCAGAGCAATCGCCTCCAGCGCTGGTTTTAACGAAt                    >  1:175817/1‑53 (MQ=255)
                                                                gTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACGTTGACCAGt  >  1:1477632/1‑71 (MQ=255)
                                                                gTTTCCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACGTTGACCAGt  <  1:3565911/71‑1 (MQ=255)
                                                                 ttttCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAGTCGGGCAACGTTGa       <  1:4125537/65‑1 (MQ=255)
                                                                 ttttCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAAc            <  1:1261730/60‑1 (MQ=255)
                                                                   ttCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGtt                             >  1:1978829/1‑41 (MQ=255)
                                                                    |                                                                  
CCAGTCGAATGGCATCTACGCTCTCTTCAAACGCTTCTGGCGACATCTTTTCTACCCGCTCGAAGTTTTCCTCAGTACCGTGCAGCGCAATCGCCTCCAGCGCTGGTTTTAACGAATCGGGCAACGTTGACCAGT  >  minE/1266887‑1267021

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