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
A4 F21 I0 R1	1009	73.8	4146436	87.4%	3623985	60.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,572,487	A→G	21.0%	intergenic (+1255/‑524)	yibH → / → ysaB	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,572,487	0	A	G	21.0%	155.8 / 38.8	76	intergenic (+1255/‑524)	yibH/ysaB	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (33/27); new base G (11/5); total (44/32)
Fisher's exact test for biased strand distribution p-value = 4.00e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TATGCCGTCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAGCGACTGG  >  minE/2572417‑2572556

tATGCCGTCATGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTa                                                                       <  1:1063346/71‑1 (MQ=255)

  tGCCGTCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGc                                                                     >  1:3826341/1‑71 (MQ=255)

    ccGTCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCa                                                                   >  1:541424/1‑71 (MQ=255)

    ccGTCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCa                                                                   >  1:3390577/1‑71 (MQ=255)

         aGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTAt                                                              >  1:3443897/1‑71 (MQ=255)

         aGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTAt                                                              >  1:500533/1‑71 (MQ=255)

         aGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTAt                                                              >  1:967463/1‑71 (MQ=255)

         aGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTAt                                                              >  1:457527/1‑71 (MQ=255)

            ttttCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCAt                                                                  <  1:2663418/64‑1 (MQ=255)

             tttCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCAt                                                                  >  1:144531/1‑63 (MQ=255)

             tttCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTta                                                           >  1:2550139/1‑70 (MQ=255)

              ttCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTtat                                                          >  1:28089/1‑70 (MQ=255)

               tCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTtata                                                         <  1:497102/70‑1 (MQ=255)

                   ttgcttgcTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATaaa                                                       <  1:1702612/68‑1 (MQ=255)

                   ttgcttgcTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATaaa                                                       <  1:4058463/68‑1 (MQ=255)

                   ttgcttgcTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAAt                                                      <  1:2029191/69‑1 (MQ=255)

                     gcttgctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTta                                                           >  1:51880/1‑62 (MQ=255)

                     gcttgctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAAtgtg                                                   <  1:279889/70‑1 (MQ=255)

                      cttgctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATgtgt                                                  <  1:3273523/70‑1 (MQ=255)

                         gctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACa                                               <  1:1365896/70‑1 (MQ=255)

                         gctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAAtgtg                                                   >  1:3155666/1‑66 (MQ=255)

                          ctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACaa                                              <  1:1898797/70‑1 (MQ=255)

                          ctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACa                                               <  1:3100369/69‑1 (MQ=255)

                               gggTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGa                                        >  1:1650687/1‑71 (MQ=255)

                                ggTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGat                                       <  1:1227866/71‑1 (MQ=255)

                                ggTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACa                                               <  1:3105336/63‑1 (MQ=255)

                                 gTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACggg                                          >  1:1870444/1‑67 (MQ=255)

                                 gTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGat                                       >  1:1648688/1‑70 (MQ=255)

                                  tCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCa                                                                   <  1:2128680/41‑1 (MQ=255)

                                  tCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATc                                                                 <  1:1329623/43‑1 (MQ=255)

                                   cATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGattat                                    >  1:3736116/1‑71 (MQ=255)

                                    aTTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGattat                                    >  1:2594531/1‑70 (MQ=255)

                                    aTTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGattat                                    >  1:2412843/1‑70 (MQ=255)

                                      tAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTAc                                                >  1:3733741/1‑56 (MQ=255)

                                      tAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTAc                                                >  1:136299/1‑56 (MQ=255)

                                      tAACATTACAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTAtttt                                 >  1:1178655/1‑71 (MQ=255)

                                       aaCATTCCAACTCCATAGGCCTTGAGGTATTAGCCa                                                                   >  1:889813/1‑36 (MQ=255)

                                       aaCATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAAtgtg                                                   >  1:694728/1‑52 (MQ=255)

                                       aaCATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAAtgtg                                                   >  1:1434506/1‑52 (MQ=255)

                                       aaCATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTAtttt                                 >  1:2902021/1‑70 (MQ=255)

                                       aaCATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTAtttt                                 >  1:2261337/1‑70 (MQ=255)

                                       aaCATTCCAACTCCATAGGCCTTCAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTAtttt                                 >  1:3259170/1‑70 (MQ=255)

                                        aCATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTa                               <  1:2776941/71‑1 (MQ=255)

                                        aCATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTa                               >  1:1900368/1‑71 (MQ=255)

                                        aCATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTa                               <  1:2001656/71‑1 (MQ=255)

                                          aTTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGattat                                    <  1:304953/64‑1 (MQ=255)

                                          aTTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTa                               <  1:1468459/69‑1 (MQ=255)

                                           ttCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACgg                                           <  1:2558635/56‑1 (MQ=255)

                                           ttCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGattatt                                   <  1:3887134/64‑1 (MQ=255)

                                            tCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACAtt                           >  1:3920581/1‑71 (MQ=255)

                                               aaCTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACAtt                           >  1:3035093/1‑68 (MQ=255)

                                                aCTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTAc                              >  1:3159552/1‑64 (MQ=255)

                                                    cATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCatat                     <  1:371115/69‑1 (MQ=255)

                                                    cATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCAtatta                   >  1:3230619/1‑71 (MQ=255)

                                                     aTAGGCCTTGAGGTATTAGCCATCTATTTATAAAtgt                                                    <  1:2038569/37‑1 (MQ=255)

                                                     aTAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTAttt                                  >  1:3877312/1‑55 (MQ=255)

                                                      tAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGatt                                      <  1:1146423/50‑1 (MQ=255)

                                                      tAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGatt                                      <  1:917084/50‑1 (MQ=255)

                                                      tAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATattatt                 <  1:1596125/71‑1 (MQ=255)

                                                        ggCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTAttttt                                <  1:2258627/54‑1 (MQ=255)

                                                         gCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTAc               >  1:14862/1‑70 (MQ=255)

                                                          ccTTGAGGTATTGGCCATCTATTTATAAATGTGTTCAACggg                                          >  1:598038/1‑42 (MQ=255)

                                                          ccTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACa                             >  1:397725/1‑55 (MQ=255)

                                                          ccTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACa                             >  1:2938181/1‑55 (MQ=255)

                                                           cTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTAc               >  1:3161938/1‑68 (MQ=255)

                                                             tGAGGTATTAGCCATCTATTTATAAATGTGTACAACggg                                          <  1:3199442/39‑1 (MQ=255)

                                                              gAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTa                               >  1:1127745/1‑49 (MQ=255)

                                                              gAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACa                             >  1:1267680/1‑51 (MQ=255)

                                                              gAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAg         >  1:322481/1‑71 (MQ=255)

                                                              gAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAg         >  1:947068/1‑71 (MQ=255)

                                                               aGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAGc        <  1:1632817/71‑1 (MQ=255)

                                                                ggTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAGCg       <  1:2715020/71‑1 (MQ=255)

                                                                 gTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAGCGa      >  1:517454/1‑71 (MQ=255)

                                                                   aTTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAGCGACt    >  1:1861309/1‑71 (MQ=255)

                                                                    ttAGCCATCTATTTATAAATGTGTACAACGGGGATTAttt                                  <  1:3937994/40‑1 (MQ=255)

                                                                    ttAGCCATCTATTTATAAATGTGTACAACGGGGATTAttt                                  <  1:3933383/40‑1 (MQ=255)

                                                                    ttAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTAc                              <  1:2808748/44‑1 (MQ=255)

                                                                      aGCCATCTATTTATAAATGTGTACAACGGGGATTAtttt                                 >  1:1138400/1‑39 (MQ=255)

                                                                      aGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAGCGACTgg  >  1:175490/1‑70 (MQ=255)

                                                                      aGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAGCGACTgg  >  1:3314929/1‑70 (MQ=255)

TATGCCGTCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAGCGACTGG  >  minE/2572417‑2572556

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