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 2,933,019 G→A 28.9% G297G (GGC→GGT)  idnT ← L‑idonate and D‑gluconate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,933,0190GA28.9% 94.7 / 46.4 66G297G (GGC→GGT) idnTL‑idonate and D‑gluconate transporter
Reads supporting (aligned to +/- strand):  ref base G (22/24);  new base A (10/9);  total (32/34)
Fisher's exact test for biased strand distribution p-value = 7.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

ACCGCTATCTACTAATACCTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTACGTCGGCCCAGTGTGAAA  >  minE/2932950‑2933088
                                                                     |                                                                     
acCGCTATCTACTAATACCTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAgcgc                                                                      >  1:1678994/1‑71 (MQ=255)
 ccGCTATCTACTAATACCTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCTcc                                                                     <  1:1199315/71‑1 (MQ=255)
   gCTATCTACTAATACCTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCACCta                                                                   <  1:597746/71‑1 (MQ=255)
       tCTACTAATACCTGCTTAAACGCTCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCTATAg                                                                <  1:711375/70‑1 (MQ=255)
       tCTACTAATACCTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCtata                                                                 <  1:2707431/69‑1 (MQ=255)
          actaATACCTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATc                                                            >  1:1112949/1‑71 (MQ=255)
             aaTACCTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCACCtata                                                                 >  1:2591719/1‑63 (MQ=255)
              aTACCTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATcccc                                                         <  1:3035257/70‑1 (MQ=255)
              aTACCTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATcccc                                                         >  1:1264999/1‑70 (MQ=255)
              aTACCTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATcccc                                                         <  1:2257496/70‑1 (MQ=255)
              aTACCTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCACCTATAGAATcccc                                                         >  1:1066493/1‑70 (MQ=255)
                  cTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGa                                                    <  1:2617188/71‑1 (MQ=255)
                   tGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGa                                                    >  1:2899582/1‑70 (MQ=255)
                     cTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCACCTATAGAATCCCCAATGgtat                                                 >  1:2886876/1‑71 (MQ=255)
                      ttAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCACCTATAGAATCCCCAATGATATc                                                >  1:1107108/1‑71 (MQ=255)
                        aaaCGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCACCTATAGAATCCCCAATGATATcc                                               <  1:2272122/70‑1 (MQ=255)
                         aaCGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCta                                                                   >  1:2104074/1‑49 (MQ=255)
                         aaCGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCAt                                             >  1:1734121/1‑71 (MQ=255)
                            gcgcCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGAt                                          >  1:3475810/1‑71 (MQ=255)
                            gcgcCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGAt                                          >  1:876970/1‑71 (MQ=255)
                             cgccgccgcCAGCGATAATAAACACAATCATCGCGATAGCACCTATAGAATCCCCAATGATATCCATGAtt                                         <  1:1980700/71‑1 (MQ=255)
                              gccgccgccAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGAttt                                        >  1:924898/1‑71 (MQ=255)
                              gccgccgccAGCGATAATAAACACAATCATCGCGATAGCACCTATAGAATCCCCAATGATATCCATGAttt                                        >  1:3830796/1‑71 (MQ=255)
                              gccgccgccAGCGATAATAAACACAATCATCGCGATAGCACCTATAGAATCCCCAATGATATCCATGAttt                                        >  1:3053386/1‑71 (MQ=255)
                               ccgccgccAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATcccc                                                         <  1:3471265/53‑1 (MQ=255)
                               ccgccgccAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTg                                       <  1:90224/71‑1 (MQ=255)
                                cgccgccAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTg                                       <  1:3905442/70‑1 (MQ=255)
                                cgccgccAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGc                                      >  1:3686884/1‑71 (MQ=255)
                                 gccgccAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAAt                                                             >  1:3460461/1‑47 (MQ=255)
                                 gccgccAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATc                                                            <  1:711260/48‑1 (MQ=255)
                                 gccgccAGCGATAAT‑AACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTg                                       <  1:1241761/68‑1 (MQ=255)
                                  ccgccAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTc                                    <  1:2366617/71‑1 (MQ=255)
                                    gccAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGa                                  <  1:3407053/71‑1 (MQ=255)
                                    gccAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGa                                  <  1:2924085/71‑1 (MQ=255)
                                      cAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGa                                                               >  1:2646539/1‑40 (MQ=255)
                                       aGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATgg                               >  1:3853876/1‑71 (MQ=255)
                                         cGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTg                             >  1:1953484/1‑71 (MQ=255)
                                           ataataAACACAATCATCGCGATAGCACCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCg                           >  1:3707642/1‑71 (MQ=255)
                                            taataaACACAATCATCGCGATAGGGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTg                             >  1:1024448/1‑68 (MQ=255)
                                             aataaACACAATCATCGCGATAGCGCCTATAGAATCCCCAAt                                                      <  1:876088/42‑1 (MQ=255)
                                             aataaACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTg                                       <  1:3545639/57‑1 (MQ=255)
                                              ataaACACAATCATCGCGATAGCACCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTcc                        <  1:474901/71‑1 (MQ=255)
                                                aaaCACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGc                            <  1:541801/65‑1 (MQ=255)
                                                 aaCACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCAt                      <  1:170814/70‑1 (MQ=255)
                                                 aaCACAATCATCGCGATAGCACCTATAGAATCCCCAATGATATCCATGa                                           <  1:301591/49‑1 (MQ=255)
                                                  acacAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGt                          >  1:709244/1‑65 (MQ=255)
                                                  acacAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTa                    >  1:2137422/1‑71 (MQ=255)
                                                   cacaATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATgg                               >  1:353267/1‑59 (MQ=255)
                                                   cacaATCATCGCGATAGCACCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTAc                   <  1:1705851/71‑1 (MQ=255)
                                                     caATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATg                                            >  1:941457/1‑44 (MQ=255)
                                                       atcatcGCGATAGCACCTATAGAATCCCCAATGATATCCATGATTTGCTCGa                                  >  1:3423015/1‑52 (MQ=255)
                                                       atcatcGCGATAGCACCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTACGTCg               <  1:1192165/71‑1 (MQ=255)
                                                        tcatcGCGATAGCGCCTATAGAATCCCCAATGATATCCATGAttt                                        >  1:958508/1‑45 (MQ=255)
                                                        tcatcGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTc                         <  1:1543831/60‑1 (MQ=255)
                                                        tcatcGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCa                       >  1:2051830/1‑62 (MQ=255)
                                                          atcGCGATAGCGCCTATAGAATCCCCAATGATATCCATGAtt                                         >  1:2658516/1‑42 (MQ=255)
                                                           tcGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGc                                      <  1:1072574/44‑1 (MQ=255)
                                                           tcGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTAc                   <  1:3086179/63‑1 (MQ=255)
                                                             gcgATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTACGTCGGCCCa          <  1:3923205/70‑1 (MQ=255)
                                                             gcgATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTACGTCGGCCCAg         >  1:2211055/1‑71 (MQ=255)
                                                              cgATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCTATGGTGCg                           <  1:880916/52‑1 (MQ=255)
                                                                aTAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTACGTCGGCCCAgtgt      <  1:1095843/71‑1 (MQ=255)
                                                                 tcgcgcCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTACGTCGGCCCAgtgt      <  1:806422/68‑1 (MQ=255)
                                                                 tAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTACGTCGGCCCAgtgt      <  1:347593/70‑1 (MQ=255)
                                                                 tAGCACCTATAGAATCCCCAATGATATCCATGATTTGc                                      <  1:483318/38‑1 (MQ=255)
                                                                 tAGCACCTATAGAATCCCCAATGATATCCATGATTTGc                                      <  1:3899485/38‑1 (MQ=255)
                                                                 tAGCACCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTACGTCGGCCCAgtgt      >  1:2127646/1‑70 (MQ=255)
                                                                 tAGCACCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTACGTCGGCCCAgtgt      >  1:1616756/1‑70 (MQ=255)
                                                                   gcgcCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTACGTCGGCCCAGtgtg     >  1:1651879/1‑69 (MQ=255)
                                                                     gcCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTACGTCGGCCCAGTGTGaaa  >  1:2621757/1‑70 (MQ=255)
                                                                     |                                                                     
ACCGCTATCTACTAATACCTGCTTAAACGCGCCGCCGCCAGCGATAATAAACACAATCATCGCGATAGCGCCTATAGAATCCCCAATGATATCCATGATTTGCTCGATGGTGCGTCCATTACGTCGGCCCAGTGTGAAA  >  minE/2932950‑2933088

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