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 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 832,097 T→C 22.6% R185R (CGT→CGC)  narG → nitrate reductase 1, alpha subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE832,0970TC22.6% 154.6 / 42.9 84R185R (CGT→CGC) narGnitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand):  ref base T (36/29);  new base C (13/6);  total (49/35)
Fisher's exact test for biased strand distribution p-value = 4.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.31e-01

AGGTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCG  >  minE/832036‑832166
                                                             |                                                                     
aggTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGt                                                              <  1:215467/71‑1 (MQ=255)
    gaacgaacTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTtct                                                          >  1:4393584/1‑71 (MQ=255)
    gaacgaacTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTtct                                                          >  1:493275/1‑71 (MQ=255)
    gaacgaacTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTtct                                                          >  1:4941474/1‑71 (MQ=255)
     aacgaacTGATCGCCGCATCTAACGTTTACACCATCAAAAATTACGGCCCGGACCGTGTCGCTGGCTtctc                                                         >  1:2628453/1‑71 (MQ=255)
     aacgaacTGATCGCCGCATCTAACGTTTACACCATCAAAAATTACGGCCCGGACCGTGTCGCTGGCTtctc                                                         >  1:4040059/1‑71 (MQ=255)
     aacgaacTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTtct                                                          <  1:131151/70‑1 (MQ=255)
     aacgaacTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTtc                                                           <  1:5481344/69‑1 (MQ=255)
       cgaacTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGc                                                       >  1:3485223/1‑71 (MQ=255)
        gaacTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGcc                                                      <  1:4976961/71‑1 (MQ=255)
           cTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAAt                                                   <  1:4964170/71‑1 (MQ=255)
              attgccgccGCTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATccc                                                <  1:3152349/68‑1 (MQ=255)
              aTCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCgtgt                                                                     <  1:4243162/50‑1 (MQ=255)
              aTCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTcc                                                >  1:936587/1‑71 (MQ=255)
               tCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCgtg                                                                      <  1:4168738/48‑1 (MQ=255)
               tCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAAt                                                   >  1:1866958/1‑67 (MQ=255)
               tCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCg                                               >  1:2305049/1‑71 (MQ=255)
                cgccgcATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTg                                                                   >  1:3150246/1‑50 (MQ=255)
                 gccgccGCTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGc                                             >  1:634764/1‑71 (MQ=255)
                 gccgccGCTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGc                                             >  1:4053174/1‑71 (MQ=255)
                 gccgcATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTCGCTGGTTTCTCGCCAATTCCGGc                                             <  1:2273519/71‑1 (MQ=255)
                   cgcATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCaa                                           >  1:123709/1‑71 (MQ=255)
                    gcATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCgtg                                                                      <  1:3474836/43‑1 (MQ=255)
                     cATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGtt                                                             >  1:2335341/1‑51 (MQ=255)
                     cATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATg                                         <  1:5015116/71‑1 (MQ=255)
                       tCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTc                                                 <  1:4360545/61‑1 (MQ=255)
                       tCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGc                                             <  1:2610061/65‑1 (MQ=255)
                       tCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGc                                             <  1:993397/65‑1 (MQ=255)
                       tCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTc                                       >  1:4559810/1‑71 (MQ=255)
                       gcTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGc                                             <  1:183876/64‑1 (MQ=255)
                       gcTAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTc                                       <  1:5170591/70‑1 (MQ=255)
                         tAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTcc                                                >  1:5432170/1‑60 (MQ=255)
                         tAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGc                                             <  1:2670855/63‑1 (MQ=255)
                         tAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGtt                                                             <  1:2404767/47‑1 (MQ=255)
                         tAACGTCTGGACCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTtct                                                          >  1:5250444/1‑50 (MQ=255)
                          aaCGTTTACACCATCAAAAACTACGGCCCGGACCgtgt                                                                     >  1:1888533/1‑38 (MQ=255)
                          aaCGTTTACACCATCAAAAACTACGGCCCGGACCgtgt                                                                     >  1:1158981/1‑38 (MQ=255)
                          aaCGTTTACACCATCAAAAACTACGGCCCGGACCgtg                                                                      >  1:3044162/1‑37 (MQ=255)
                          aaCGTTTACACCATCAAAAACTACGGCCCGGACCgtg                                                                      >  1:1733049/1‑37 (MQ=255)
                          aaCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCg                                      >  1:517407/1‑69 (MQ=255)
                          aaCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGAt                                    >  1:317158/1‑71 (MQ=255)
                           aCGTTTACACCATCAAAAACTACGGCCCGGACCgtgt                                                                     <  1:2798108/37‑1 (MQ=255)
                           aCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCg                                               <  1:3344827/59‑1 (MQ=255)
                           aCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCaa                                           >  1:2961017/1‑63 (MQ=255)
                           aCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTc                                       <  1:2022767/67‑1 (MQ=255)
                           aCGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTc                                       <  1:3704031/67‑1 (MQ=255)
                            cGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTtctc                                                         >  1:2013047/1‑48 (MQ=255)
                             gTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGt                                 >  1:1435766/1‑71 (MQ=255)
                              tttACACCATCAAAAACTACGGCCCGGACCGTGTTGc                                                                  <  1:1025657/37‑1 (MQ=255)
                              tttACACCATCAAAAACTACGGCCCGGACCGTGTTGCt                                                                 <  1:5180480/38‑1 (MQ=255)
                              tttACACCATCAAAAACTACGGCCCGGACCGTGTTGCt                                                                 <  1:3931721/38‑1 (MQ=255)
                              tttACACCATCAAAAACTACGGCCCGGACCGTGTTGCt                                                                 <  1:3938579/38‑1 (MQ=255)
                               ttACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGtt                                >  1:3071241/1‑70 (MQ=255)
                                tACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATg                                         >  1:3673520/1‑60 (MQ=255)
                                tACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGttt                               <  1:3578637/70‑1 (MQ=255)
                                tACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGttt                               <  1:2123143/70‑1 (MQ=255)
                                  gacCATCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATGGTTTCt                             >  1:1141376/2‑70 (MQ=255)
                                  cacCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCtt                            <  1:1033628/71‑1 (MQ=255)
                                  cacCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCt                             <  1:3327177/70‑1 (MQ=255)
                                     cATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAAt                                                   >  1:4634210/1‑45 (MQ=255)
                                     cATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCtt                            >  1:15918/1‑68 (MQ=255)
                                     cATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa                           >  1:64348/1‑69 (MQ=255)
                                     cATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCAGGCAATGTCGATGGTTTCTTACg                         >  1:89437/1‑71 (MQ=255)
                                      aTCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATgg                                  <  1:3825966/61‑1 (MQ=255)
                                      aTCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATGGTTTc                              <  1:4413210/65‑1 (MQ=255)
                                       tCAAAACCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGATGGTTTCTTACGcc                       >  1:4959062/1‑70 (MQ=255)
                                       tCAAAACCTACGGCCCGGATCGCGATGCCGGTTtc                                                           >  1:2449897/1‑35 (MQ=12)
                                       tCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTc                                                 <  1:4729009/45‑1 (MQ=255)
                                       tCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCa                       <  1:4060976/71‑1 (MQ=255)
                                       tCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCa                       >  1:4398508/1‑71 (MQ=255)
                                       tCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCa                       >  1:687530/1‑71 (MQ=255)
                                        cAAAACCTACGGCCCGGATCGCGTTGCCGGTTtct                                                          >  1:2846002/1‑35 (MQ=19)
                                        cAAAACCTACGGCCCGGATCGCGTTGCCGGTTtct                                                          >  1:1182619/1‑35 (MQ=19)
                                        cAAAACCTACGGCCCGGATCGCGTTGCCGGTTtct                                                          >  1:3613328/1‑35 (MQ=19)
                                         aaaacCTACGGCCCGGATCGCGTTGCCGGTATCTCGCCGATCCCGGCGATGTCGATGGTTTCTTACGccgc                     >  1:5204152/1‑68 (MQ=255)
                                         aaaaaCTACGGCCCGGACCGTGTTGCTGGTTtctc                                                         >  1:1357552/1‑35 (MQ=255)
                                         aaaaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa                           >  1:4121883/1‑65 (MQ=255)
                                         aaaaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa                           >  1:4345175/1‑65 (MQ=255)
                                         aaaaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa                           >  1:911313/1‑65 (MQ=255)
                                         aaaaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCAt                      <  1:2540267/70‑1 (MQ=255)
                                          aaacCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGcga                                           >  1:12496/1‑46 (MQ=255)
                                          aaacCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCGGCGATGTCGa                                     >  1:5329077/1‑54 (MQ=255)
                                          aaaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATgg                                  >  1:105675/1‑57 (MQ=255)
                                          aaaaCTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATgg                                  >  1:4079964/1‑57 (MQ=255)
                                           aaaCTACGGCCCGGATCGCGTTGCCGGTTTCTCGCCGATCCCgg                                              >  1:141378/1‑44 (MQ=25)
                                                    cccGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACg            >  1:3754798/1‑69 (MQ=255)
                                                     ccGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCt          >  1:1641594/1‑70 (MQ=255)
                                                        gACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCa                       <  1:4593028/54‑1 (MQ=255)
                                                          ccGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTAtctct    >  1:3760901/1‑71 (MQ=255)
                                                           cGTGTTGCTGGTTTCTCTCCAATTCCGGCAATGTCGATGGTTTCt                             <  1:5041481/45‑1 (MQ=255)
                                                           cGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCt                             <  1:4416514/45‑1 (MQ=255)
                                                           cGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTAtctctc   <  1:432230/71‑1 (MQ=255)
                                                             tgtTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa                           >  1:2281001/1‑45 (MQ=255)
                                                             tgtTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTa                           >  1:4226510/1‑45 (MQ=255)
                                                             tgtTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCg  >  1:5561017/1‑70 (MQ=255)
                                                             tgtTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCg  >  1:4606854/1‑70 (MQ=255)
                                                             |                                                                     
AGGTGAACGAACTGATCGCCGCATCTAACGTTTACACCATCAAAAACTACGGCCCGGACCGTGTTGCTGGTTTCTCGCCAATTCCGGCAATGTCGATGGTTTCTTACGCATCGGGTGCACGCTATCTCTCG  >  minE/832036‑832166

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