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	636,861	G→A	37.9%	V1279V (GTG→GTA)	mukB →	fused chromosome partitioning proteins

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	636,861	0	G	A	37.9%	26.4 / 28.6	50	V1279V (GTG→GTA)	mukB	fused chromosome partitioning proteins
Reads supporting (aligned to +/- strand): ref base G (25/6); new base A (17/2); total (42/8)
Fisher's exact test for biased strand distribution p-value = 6.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.72e-01

CAACCAGGGGTTGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGATGTGCTCTCTGAACAGCACGAGCAGCATC  >  minE/636798‑636916

cAACCAGGGGTTGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGa                                                    <  1:65708/69‑1 (MQ=255)

cAACCAGGGGTTGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGa                                                    <  1:178423/69‑1 (MQ=255)

      gtggTTGCAGAACGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAacgca                                              <  1:2324041/67‑1 (MQ=255)

      ggggTTGCAGAACGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAacgca                                              <  1:209567/69‑1 (MQ=255)

           tGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGcc                                          >  1:2376107/1‑68 (MQ=255)

           tGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGcc                                          >  1:714900/1‑68 (MQ=255)

           tGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCa                                         >  1:1000140/1‑69 (MQ=255)

           tGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCa                                         >  1:2602740/1‑69 (MQ=255)

           tGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCa                                         >  1:323119/1‑69 (MQ=255)

           tGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCa                                         >  1:1995542/1‑69 (MQ=255)

           tGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCa                                         >  1:1828048/1‑69 (MQ=255)

           tGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCa                                         >  1:1706891/1‑69 (MQ=255)

           tGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCa                                         >  1:1604302/1‑69 (MQ=255)

            gCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCAt                                        <  1:3433839/69‑1 (MQ=255)

            gCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCAt                                        <  1:3373915/69‑1 (MQ=255)

             cAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGa                                                    <  1:491180/56‑1 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGTCATGCtg                                    >  1:665822/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:30678/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:444230/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:3327198/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:3344189/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:3386944/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:374859/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:2840384/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:921127/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:971496/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:2753598/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:1429371/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:152387/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:2536804/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:2280454/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCtg                                    >  1:28173/1‑68 (MQ=255)

                aaCGTATCGTTTGGCCAGGTGAACAGCGTACGTCTGAACGTGAACGTACGTGAAACGCACGCCATGCt                                     >  1:2598300/1‑68 (MQ=255)

                   gTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTg                                 <  1:2710583/69‑1 (MQ=255)

                      tCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACTTGAACGTGCGTGAAACGCACGCCATGCTACTGGAt                              >  1:2034366/1‑69 (MQ=255)

                      tCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGAt                              >  1:2532771/1‑69 (MQ=255)

                      tCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGAt                              >  1:771969/1‑69 (MQ=255)

                      tCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGAt                              >  1:1731215/1‑69 (MQ=255)

                      tCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGAt                              >  1:507706/1‑69 (MQ=255)

                      tCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGAt                              >  1:2178640/1‑69 (MQ=255)

                      tCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGAt                              >  1:400830/1‑69 (MQ=255)

                      tCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGAt                              >  1:3427327/1‑69 (MQ=255)

                      tCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGAt                              >  1:3287140/1‑69 (MQ=255)

                      tCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGAt                              >  1:2701611/1‑69 (MQ=255)

                      tCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGAt                              >  1:2912774/1‑69 (MQ=255)

                                    gAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGATGTGCTCTCTGAAc                 >  1:2566288/1‑68 (MQ=255)

                                    gAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGATGTGCTCTCTGAAc                 >  1:325110/1‑68 (MQ=255)

                                    gAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGATGTGCTCTCTGAAc                 >  1:1696169/1‑68 (MQ=255)

                                    gAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGATGTGCTCTCTGAAc                 >  1:3101440/1‑68 (MQ=255)

                                    gAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGATGTGCTCTCTGAAc                 >  1:1013241/1‑68 (MQ=255)

                                                          aacgtgCGTGAAACGCACGCCATGCTACTGGATGTGCTCTCTGAACAGCACGAGCAGCATc  <  1:257037/61‑1 (MQ=255)

                                                          aacgtgCGTGAAACGCACGCCATGCTACTGGATGTGCTCTCTGAACAGCACGAGCAGCATc  <  1:497089/61‑1 (MQ=255)

                                                          aacgtgCGTGAAACGCACGCCATGCTACTGGATGTGCTCTCTGAACAGCACGAGCAGCATc  <  1:3231350/61‑1 (MQ=255)

                                                          aacgtgCGTGAAACGCACGCCATGCTACTGGATGTGCTCTCTGAACAGCACGAGCAGCATc  <  1:774749/61‑1 (MQ=255)

CAACCAGGGGTTGCAGAACGTATCGTTTGGTCAGGTGAACAGCGTGCGTCTCAACGTGAACGTGCGTGAAACGCACGCCATGCTACTGGATGTGCTCTCTGAACAGCACGAGCAGCATC  >  minE/636798‑636916

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