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	2,572,487	A→G	84.4%	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	84.4%	146.9 / 17.3	64	intergenic (+1255/‑524)	yibH/ysaB	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (6/4); new base G (26/28); total (32/32)
Fisher's exact test for biased strand distribution p-value = 7.32e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.90e-01

TATGCCGTCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAG  >  minE/2572417‑2572549

tATGCCGTCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTa                                                                <  1:4029320/71‑1 (MQ=255)

       tCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCt                                                         <  1:3882132/71‑1 (MQ=255)

         aGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTAt                                                       >  1:3553373/1‑71 (MQ=255)

          ggTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTAtt                                                      >  1:5448701/1‑71 (MQ=255)

            ttttCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTta                                                    <  1:5536577/71‑1 (MQ=255)

              ttCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGc                                                              >  1:94035/1‑59 (MQ=255)

              ttCTATAGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTtat                                                   >  1:5667/1‑70 (MQ=255)

               tCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTtata                                                  >  1:4140031/1‑70 (MQ=255)

               tCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTtat                                                   >  1:1540419/1‑69 (MQ=255)

               tCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTtata                                                  <  1:1227357/70‑1 (MQ=255)

                cTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATaa                                                 <  1:4190942/70‑1 (MQ=255)

                cTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATaaa                                                >  1:978776/1‑71 (MQ=255)

                   ttgcttgcTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAAt                                               <  1:2211383/69‑1 (MQ=255)

                     gcttgctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAAtgt                                             >  1:5503763/1‑69 (MQ=255)

                      cttgctCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTa                                          >  1:3599723/1‑71 (MQ=255)

                             ccGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATc                                                          <  1:5044651/48‑1 (MQ=255)

                             ccGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATc                                                          <  1:331185/48‑1 (MQ=255)

                             ccGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACggg                                   >  1:1335145/1‑71 (MQ=255)

                             ccGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACg                                     <  1:4090185/69‑1 (MQ=255)

                               gggTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTa                                                        >  1:3479412/1‑48 (MQ=255)

                               gggTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGa                                 >  1:519007/1‑71 (MQ=255)

                                   cATTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGattat                             >  1:1348344/1‑71 (MQ=255)

                                   aaTTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGattat                             >  1:3931969/2‑71 (MQ=255)

                                    aTTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACa                                        >  1:818583/1‑59 (MQ=255)

                                    aTTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACa                                        >  1:383397/1‑59 (MQ=255)

                                    aTTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACa                                        >  1:3542414/1‑59 (MQ=255)

                                    aTTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACa                                        >  1:2467320/1‑59 (MQ=255)

                                    aTTAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGattatt                            <  1:3278587/71‑1 (MQ=255)

                                     ttAACATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTtata                                                  <  1:4781212/48‑1 (MQ=255)

                                     ttAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAAtgtg                                            <  1:643494/54‑1 (MQ=255)

                                       aaCATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTtata                                                  >  1:2593069/1‑46 (MQ=255)

                                       aaCATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTAtttt                          <  1:4848259/70‑1 (MQ=255)

                                       aaCATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTAtttt                          >  1:1243892/1‑70 (MQ=255)

                                       aaCATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTAtttt                          >  1:1788047/1‑70 (MQ=255)

                                       aaCATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTAtttt                          <  1:5594875/70‑1 (MQ=255)

                                       aaCATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTtata                                                  <  1:2968348/46‑1 (MQ=255)

                                       aaCATTCCAACTCCATAGACCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTAtttt                          >  1:5387902/1‑70 (MQ=255)

                                        aCATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTAt                                                       >  1:5627467/1‑40 (MQ=255)

                                        aCATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTAt                                                       >  1:4558943/1‑40 (MQ=255)

                                        aCATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTAt                                                       >  1:1848423/1‑40 (MQ=255)

                                        aCATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTa                        <  1:2024440/71‑1 (MQ=255)

                                        aCATTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTa                        <  1:1919864/71‑1 (MQ=255)

                                        aCATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTa                        <  1:3337465/71‑1 (MQ=255)

                                          aTTCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACa                      <  1:2937136/71‑1 (MQ=255)

                                           ttCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTtat                                                   <  1:1407856/41‑1 (MQ=255)

                                            tCCAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACAtt                    >  1:4876296/1‑71 (MQ=255)

                                             ccAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTg                   >  1:4888110/1‑71 (MQ=255)

                                              cAACTCCATAGGCCTTGAGGTATTGGCCATCTATTtat                                                   <  1:2583027/38‑1 (MQ=255)

                                              cAACTCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGc                  <  1:4614262/71‑1 (MQ=255)

                                                  tCCATAGGCCTTGAGGTATTGTCCATCTATTtata                                                  <  1:3370232/35‑1 (MQ=255)

                                                  tCCATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCat                <  1:1584871/69‑1 (MQ=255)

                                                    cATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCatat              <  1:783681/69‑1 (MQ=255)

                                                    cATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCAtatta            >  1:897525/1‑71 (MQ=255)

                                                    cATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCAtatta            <  1:3183598/71‑1 (MQ=255)

                                                    cATAGGCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCAtatt             <  1:2374895/70‑1 (MQ=255)

                                                        ggCCTTGAGGTATTGGCCATCTATTTATAAATTTGTACAACGGGGATTAtttt                          <  1:1947986/53‑1 (MQ=255)

                                                        ggCCTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATAttgtta         <  1:721863/70‑1 (MQ=255)

                                                           cTTGAGGTATTGGCCATCTATTTATAAATGTGTAc                                         <  1:217093/35‑1 (MQ=255)

                                                           cTTGAGGTATTGGCCATCTATTTATAAATGTGTAc                                         <  1:574474/35‑1 (MQ=255)

                                                           cTTGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATattatt          <  1:1981553/66‑1 (MQ=255)

                                                             tGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTAc                       >  1:1598521/1‑51 (MQ=255)

                                                             tGAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTAc                       >  1:3993435/1‑51 (MQ=255)

                                                              gAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGa    <  1:4009247/69‑1 (MQ=255)

                                                              gAGGTATTGGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAg  >  1:2666812/1‑71 (MQ=255)

                                                              gAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGattat                             >  1:485092/1‑44 (MQ=255)

TATGCCGTCAGGTTTTCTATTGCTTGCTCCCGGGTCATTAACATTCCAACTCCATAGGCCTTGAGGTATTAGCCATCTATTTATAAATGTGTACAACGGGGATTATTTTTACATTGCATATTATTACCAGAAG  >  minE/2572417‑2572549

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