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	835,236	G→A	22.6%	D1232N (GAC→AAC)	narG →	nitrate reductase 1, alpha subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	835,236	0	G	A	22.6%	179.0 / 48.7	93	D1232N (GAC→AAC)	narG	nitrate reductase 1, alpha subunit
Reads supporting (aligned to +/- strand): ref base G (35/37); new base A (13/8); total (48/45)
Fisher's exact test for biased strand distribution p-value = 3.28e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.02e-01

CTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGG  >  minE/835166‑835305

cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTg                                                                        <  1:3580214/71‑1 (MQ=255)

cTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTg                                                                        <  1:1633377/71‑1 (MQ=255)

  ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                                                      >  1:2248875/1‑71 (MQ=255)

  ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                                                      >  1:110190/1‑71 (MQ=255)

  ttAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAAc                                                                      >  1:2657265/1‑71 (MQ=255)

   tAACTACTACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACt                                                                     >  1:3348933/1‑71 (MQ=255)

    aaCTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTg                                                                    >  1:48316/1‑71 (MQ=255)

     actactACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTgg                                                                   <  1:914913/71‑1 (MQ=255)

     actactACGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTgg                                                                   >  1:1627332/1‑71 (MQ=255)

      ctactaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggc                                                                  >  1:3641095/1‑70 (MQ=255)

         ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                                <  1:2382585/70‑1 (MQ=255)

         ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                                <  1:3220800/70‑1 (MQ=255)

         ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                                <  1:1907475/70‑1 (MQ=255)

         ctaTGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTa                                                                <  1:3456589/70‑1 (MQ=255)

         ctaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggctg                                                                <  1:1429012/70‑4 (MQ=255)

         ctaCGGCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTggctg                                                                >  1:2086464/1‑67 (MQ=255)

           acggCACCGTCGGATCGAACCGCGATGAGTTCATCATGATCCGCAAGATGAAGAACGTTAACTGGCTGGAt                                                             >  1:2152391/3‑71 (MQ=255)

            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                                                                       >  1:3271910/1‑60 (MQ=255)

            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                                                                       >  1:1677448/1‑60 (MQ=255)

            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                                                                       >  1:2879013/1‑60 (MQ=255)

            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGa                                                                       >  1:543449/1‑60 (MQ=255)

            tGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                                             <  1:1095397/70‑1 (MQ=255)

                 ccGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAGGAACATTGACTGGTTAGATGGCGaa                                                       <  1:487614/71‑1 (MQ=255)

                 ccGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGaa                                                       <  1:725893/71‑1 (MQ=255)

                    tAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGc                                                    <  1:464788/71‑1 (MQ=255)

                       gTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                                                  <  1:1175320/54‑1 (MQ=255)

                        ttCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATg                                                <  1:1214518/71‑1 (MQ=255)

                         tCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                                            >  1:1144809/1‑58 (MQ=255)

                           tAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                                                 >  1:82640/1‑67 (MQ=255)

                            aaCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                                                 <  1:2957897/66‑1 (MQ=255)

                             aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                                            >  1:2595832/1‑54 (MQ=255)

                             aCCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATg                                                            <  1:2070912/54‑1 (MQ=255)

                             aCCGAGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                                                 >  1:2624426/1‑65 (MQ=255)

                              ccGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAAt                                                 >  1:1615579/1‑64 (MQ=255)

                              ccGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAg                                           <  1:3194256/70‑1 (MQ=255)

                               cgcgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTg                                                                    >  1:3157168/1‑44 (MQ=255)

                               cgcgATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGt                                         <  1:3802636/71‑1 (MQ=255)

                                  gatgatTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACa                                      <  1:652433/71‑1 (MQ=255)

                                  gATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                                                        <  1:3853295/53‑1 (MQ=255)

                                  gATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                                                        <  1:3274004/53‑1 (MQ=255)

                                  gATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGa                                                        <  1:370518/53‑1 (MQ=255)

                                   aTGAGTTTGTTGTAGTGTGTAAGATGAAGAACATTGACTg                                                                    <  1:251812/40‑1 (MQ=255)

                                   aTGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAg                                     <  1:853548/71‑1 (MQ=255)

                                     gAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                                                  >  1:1997888/1‑40 (MQ=255)

                                     gAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGt                                                                  >  1:1693123/1‑40 (MQ=255)

                                     gAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAg                                     >  1:959944/1‑69 (MQ=255)

                                      aGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCaa                                                  >  1:3146941/1‑55 (MQ=255)

                                      aGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGga                                   <  1:1839570/70‑1 (MQ=255)

                                      aGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGga                                   <  1:3819905/70‑1 (MQ=255)

                                         ttgttgTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGgaga                                 >  1:2702740/1‑69 (MQ=255)

                                         ttgttgTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGgaga                                 >  1:780615/1‑69 (MQ=255)

                                          tgttgtAGTGCGTAAGATGAAGAACATTGACTGGtt                                                                 <  1:3228479/36‑1 (MQ=255)

                                          tgttgtAGTGCGTAAGATGAAGAACATTGACTGGtt                                                                 <  1:3509032/36‑1 (MQ=255)

                                          tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGaa                                                       >  1:3896716/1‑46 (MQ=255)

                                          tgttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCg                              >  1:541158/1‑71 (MQ=255)

                                           gttgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCg                              >  1:3855325/1‑70 (MQ=255)

                                             tgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAg                                     >  1:3705822/1‑61 (MQ=255)

                                             tgtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑Ta                           >  1:3829155/1‑70 (MQ=255)

                                              gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGa                                                              >  1:294759/1‑35 (MQ=255)

                                              gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGAt                                                             >  1:79511/1‑36 (MQ=255)

                                              gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAg                                     >  1:1157715/1‑60 (MQ=255)

                                              gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑Taa                          <  1:2938315/70‑1 (MQ=255)

                                              gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑Taa                          >  1:328648/1‑70 (MQ=255)

                                              gtAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑Taa                          >  1:3759474/1‑70 (MQ=255)

                                               tAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCa                                            <  1:3943261/52‑1 (MQ=255)

                                               tAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCa                                            <  1:1170022/52‑1 (MQ=255)

                                               tAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑Taaa                         <  1:3301694/70‑1 (MQ=255)

                                                aGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑Taaaa                        <  1:2017284/70‑1 (MQ=255)

                                                aGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAAt                       >  1:3537989/1‑71 (MQ=255)

                                                  tGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTAc                                       <  1:504547/54‑1 (MQ=255)

                                                  tGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTAc                                       <  1:3371468/54‑1 (MQ=255)

                                                   gCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGa                     >  1:2445047/1‑70 (MQ=255)

                                                    cgcaaGATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGaaa                   <  1:2209642/68‑1 (MQ=255)

                                                    cgcaaGATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGaaa                   <  1:1657235/68‑1 (MQ=255)

                                                    cGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAg                                                      >  1:2462320/1‑37 (MQ=255)

                                                     gcaaGATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGga                                   >  1:765425/3‑55 (MQ=255)

                                                      tAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGa                     <  1:3772670/67‑1 (MQ=255)

                                                      tAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAAt                 <  1:751456/71‑1 (MQ=255)

                                                      tAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGAG‑TAAAATGAAAAt                 <  1:3862461/71‑1 (MQ=255)

                                                      caaGATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGgagg                                 >  1:431940/2‑55 (MQ=255)

                                                      caaGATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAAt                 >  1:2576504/2‑71 (MQ=255)

                                                      caaGATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAAt                 >  1:3320715/2‑71 (MQ=255)

                                                        aGATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAAtcc               >  1:2944020/1‑69 (MQ=255)

                                                        aGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATg                                                >  1:138884/1‑39 (MQ=255)

                                                        aGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGga                                   >  1:2597219/1‑52 (MQ=255)

                                                        aGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTc               <  1:1001081/71‑1 (MQ=255)

                                                        aGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTc               >  1:614527/1‑71 (MQ=255)

                                                        aGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTc               >  1:3828491/1‑71 (MQ=255)

                                                         gATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAATCCg              <  1:148799/71‑1 (MQ=255)

                                                         gATGAAGAACGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAATCCg              <  1:1923858/71‑1 (MQ=255)

                                                             aagaaCGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTca          <  1:1018540/71‑1 (MQ=255)

                                                              agaaCGTTAACTGGCTGGATGATGAAGGTCGCGATCAGGTACAGGAG‑GCGAAAAAATGAAAATCCGTTcac         <  1:1445858/71‑1 (MQ=255)

                                                               gaaCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTcac         <  1:1311226/70‑1 (MQ=255)

                                                                 aCATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTc               >  1:2275607/1‑62 (MQ=255)

                                                                   aTTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGaaaa                  <  1:3940656/57‑1 (MQ=255)

                                                                      gACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCgg  <  1:1714093/70‑1 (MQ=255)

                                                                      gACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCgg  <  1:3132414/70‑1 (MQ=255)

CTTTAACTACTATGGCACCGTAGGTTCTAACCGCGATGAGTTTGTTGTAGTGCGTAAGATGAAGAACATTGACTGGTTAGATGGCGAAGGCAATGACCAGGTACAGGAGAGCG‑TAAAATGAAAATTCGTTCACAAGTCGG  >  minE/835166‑835305

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A