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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	547,042	C→T	44.0%	L55L (CTG→TTG)	ybiT →	fused predicted transporter subunits and ATP‑binding components of ABC superfamily

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	547,042	0	C	T	44.0%	14.2 / 43.6	59	L55L (CTG→TTG)	ybiT	fused predicted transporter subunits and ATP‑binding components of ABC superfamily
Reads supporting (aligned to +/- strand): ref base C (10/23); new base T (15/11); total (25/34)
Fisher's exact test for biased strand distribution p-value = 6.22e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTAAACTGCGTCAGGATCAGTTTGCCTTTGAA  >  minE/546986‑547110

aCGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACTTAGAGCCGACGTTGGGTAACGttt                                                          <  1:1919251/69‑1 (MQ=255)

aCGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACTTAGAGCCGACGTTGGGTAACGttt                                                          <  1:2165851/69‑1 (MQ=255)

aCGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACTTAGAGCCGACGTTGGGTAACGttt                                                          <  1:125110/69‑1 (MQ=255)

aCGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACTTAGAGCCGACGTTGGGTAACGttt                                                          <  1:1301549/69‑1 (MQ=255)

aCGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACTTAGAGCCGACGTTGGGTAACGttt                                                          <  1:1379260/69‑1 (MQ=255)

aCGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACTTAGAGCCGACGTTGGGTAACGttt                                                          <  1:1475956/69‑1 (MQ=255)

aCGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACTTAGAGCCGACGTTGGGTAACGttt                                                          <  1:2928267/69‑1 (MQ=255)

aCGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACTTAGAGCCGACGTTGGGTAACGttt                                                          <  1:1484154/69‑1 (MQ=255)

aCGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACTTAGAGCCGACGTTGGGTAACGttt                                                          <  1:3236843/69‑1 (MQ=255)

aCGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACTTAGAGCCGACGTTGGGTAACGttt                                                          <  1:3405867/69‑1 (MQ=255)

 cGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACTTAGAGCCGACGTTGGGTAACGttt                                                          <  1:3408560/68‑1 (MQ=255)

        ggTAAATCCACCTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGAt                                                  >  1:1631016/1‑69 (MQ=255)

         gTAAATCCACCTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGAt                                                  >  1:380891/1‑68 (MQ=255)

         gTAAATCCACCTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGAt                                                  >  1:2537268/1‑68 (MQ=255)

          tAAATCCACCTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATc                                                 >  1:572330/1‑68 (MQ=255)

            aaTCCACCTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCa                                              <  1:973050/69‑1 (MQ=255)

            aaTCCACCTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCa                                              <  1:2402373/69‑1 (MQ=255)

            aaTCCACCTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCa                                              <  1:50728/69‑1 (MQ=255)

            aaTCCACCTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCa                                              <  1:1716934/69‑1 (MQ=255)

              tCCACCTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCa                                              >  1:842149/1‑67 (MQ=255)

                   cTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:1647193/69‑1 (MQ=255)

                   cTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:317819/69‑1 (MQ=255)

                   cTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:787968/69‑1 (MQ=255)

                   cTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:2171757/69‑1 (MQ=255)

                   cTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:594138/69‑1 (MQ=255)

                   cTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:303317/69‑1 (MQ=255)

                   cTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:1194623/69‑1 (MQ=255)

                    tttATGAAGATCCTCGGCGGCGACGTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:1481523/68‑1 (MQ=255)

                    tttATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:310788/68‑1 (MQ=255)

                    tttATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:2533959/68‑1 (MQ=255)

                    tttATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:2721739/68‑1 (MQ=255)

                            gATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTa                               <  1:589151/68‑1 (MQ=255)

                               ccTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:1043141/57‑1 (MQ=255)

                               ccTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTAAACt                           >  1:2550156/1‑69 (MQ=255)

                               ccTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTAAACt                           >  1:2515002/1‑69 (MQ=255)

                               ccTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTAAACt                           >  1:2166705/1‑69 (MQ=255)

                               ccTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTAAACt                           >  1:815154/1‑69 (MQ=255)

                               ccTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTAAACt                           >  1:1920182/1‑69 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCaa                                             >  1:3383160/1‑42 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:1169874/1‑54 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:449268/1‑54 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:428901/1‑54 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:1795971/1‑54 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:1564694/1‑54 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:3055717/1‑54 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:3032047/1‑54 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:1679372/1‑54 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:2712624/1‑54 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:1688827/1‑54 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:1960738/1‑54 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:195737/1‑54 (MQ=255)

                                        cgACTTAGAGCCGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:1764699/1‑54 (MQ=255)

                                        cgACTTAGAGACGACGTTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTgg                                 >  1:1559444/1‑54 (MQ=255)

                                           ccTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:821530/45‑1 (MQ=255)

                                            ctggAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTAAACTGCGTCAGGATCAg              <  1:1728808/66‑1 (MQ=255)

                                            cTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTAAACTGCGTCAGGATCAg              <  1:3394570/69‑1 (MQ=255)

                                            cTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTAAACTGCGTCAGGATCAg              <  1:89854/69‑1 (MQ=255)

                                             ttGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTAAACTGCGTCAGGATCAg              <  1:2592307/68‑1 (MQ=255)

                                                    gACGCTGGGTAACGTTTCCCTCGATCCCAACGAgcg                                       <  1:3072650/36‑1 (MQ=255)

                                                        cTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTAAACTGCGTCAGGATCAGTTTGCCTTTGaa  <  1:1687737/69‑1 (MQ=255)

ACGGTAGTGGTAAATCCACCTTTATGAAGATCCTCGGCGGCGACCTTGAGCCGACGCTGGGTAACGTTTCCCTCGATCCCAACGAGCGCATTGGTAAACTGCGTCAGGATCAGTTTGCCTTTGAA  >  minE/546986‑547110

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