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	1,920,408	G→C	28.0%	L164L (CTC→CTG)	ygeD ←	predicted inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,920,408	0	G	C	28.0%	106.6 / 49.6	82	L164L (CTC→CTG)	ygeD	predicted inner membrane protein
Reads supporting (aligned to +/- strand): ref base G (37/22); new base C (4/19); total (41/41)
Fisher's exact test for biased strand distribution p-value = 4.20e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-01

TGGGAATGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAA  >  minE/1920344‑1920474

tGGGAATGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGa                                                                <  1:2843630/69‑1 (MQ=255)

tGGGAATGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGa                                                                <  1:2423409/69‑1 (MQ=255)

tGGGAATGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGa                                                                <  1:3410844/69‑1 (MQ=255)

      tGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGcc                                                          >  1:519682/1‑69 (MQ=255)

        tAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGCCGAGGACATGCCa                                                         >  1:1798736/1‑68 (MQ=255)

        tAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCa                                                         >  1:2458110/1‑68 (MQ=255)

        tAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCa                                                         >  1:1321901/1‑68 (MQ=255)

        tAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCa                                                         >  1:2863233/1‑68 (MQ=255)

        tAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCa                                                         >  1:1592896/1‑68 (MQ=255)

        tAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCa                                                         >  1:885825/1‑68 (MQ=255)

            tatTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTca                                                     <  1:965174/68‑1 (MQ=255)

            tatTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTca                                                     <  1:3271583/68‑1 (MQ=255)

            tatTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTca                                                     <  1:422623/68‑1 (MQ=255)

            tatTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTca                                                     <  1:846421/68‑1 (MQ=255)

            tatTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTca                                                     <  1:1623960/68‑1 (MQ=255)

              ttGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTcagcc                                                  >  1:776595/1‑69 (MQ=255)

              ttGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTcagcc                                                  >  1:3362523/1‑69 (MQ=255)

              ttGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTcagcc                                                  >  1:2824164/1‑69 (MQ=255)

              ttGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTcagcc                                                  >  1:1752968/1‑69 (MQ=255)

                ggCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTcagccag                                                >  1:419981/1‑69 (MQ=255)

                ggCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTcagccag                                                >  1:540462/1‑69 (MQ=255)

                ggCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTcagccag                                                >  1:30587/1‑69 (MQ=255)

                ggCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTcagccag                                                >  1:3195191/1‑69 (MQ=255)

                ggCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTcagccag                                                >  1:669932/1‑69 (MQ=255)

                ggCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTcagccag                                                >  1:2281676/1‑69 (MQ=255)

                ggCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTcagccag                                                >  1:2128714/1‑69 (MQ=255)

                ggCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTcagccag                                                >  1:954076/1‑69 (MQ=255)

                   aaCGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGcac                                             <  1:482037/69‑1 (MQ=255)

                         cGCACCACCGTAGGCCAGTTCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCAcaccac                                        >  1:288377/1‑68 (MQ=255)

                         cGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGcac                                             <  1:1820520/63‑1 (MQ=255)

                         cGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACaccacc                                       >  1:2805444/1‑69 (MQ=255)

                         cGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACaccacc                                       >  1:175435/1‑69 (MQ=255)

                               accGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATg                                                            <  1:599652/42‑1 (MQ=255)

                               accGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATg                                                            <  1:248103/42‑1 (MQ=255)

                               accGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATg                                                            <  1:3389164/42‑1 (MQ=255)

                               accGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATg                                                            <  1:1977203/42‑1 (MQ=255)

                               accGTAGGCCAGTGCGCATGCGGCCAGGGCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTa                                  >  1:3017972/1‑68 (MQ=255)

                               accGTAGGCCAGTGCGCATGCGGCCAGGGCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTa                                  >  1:1182093/1‑68 (MQ=255)

                               accGTAGGCCAGTGCGCATGCGGCCAGGGCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTa                                  >  1:2559912/1‑68 (MQ=255)

                               accGTAGGCCAGTGCGCATGCGGCCAGGGCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTa                                  >  1:1055469/1‑68 (MQ=255)

                                 cGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGa                                                                <  1:969802/36‑1 (MQ=255)

                                           tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa                     >  1:1286423/1‑69 (MQ=255)

                                           tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa                     >  1:1180425/1‑69 (MQ=255)

                                           tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa                     >  1:499807/1‑69 (MQ=255)

                                           tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa                     >  1:1850487/1‑69 (MQ=255)

                                           tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa                     >  1:1900454/1‑69 (MQ=255)

                                           tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa                     >  1:2356292/1‑69 (MQ=255)

                                           tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa                     >  1:2330254/1‑69 (MQ=255)

                                           tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa                     >  1:1937302/1‑69 (MQ=255)

                                           tGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaa                     >  1:75424/1‑69 (MQ=255)

                                             cgcATGCGGCCAGGGCGCCGAGGAAATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaaaa                   >  1:1479506/1‑69 (MQ=255)

                                             cgcATGCGGCCAGGGCGACGAGGAAATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCaaaa                   >  1:1483272/1‑69 (MQ=255)

                                                   cGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGa                              <  1:251683/52‑1 (MQ=255)

                                                   cGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATcgcc              >  1:1815907/1‑68 (MQ=255)

                                                   cGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATcgcc              >  1:2510034/1‑68 (MQ=255)

                                                   cGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATcgcc              >  1:1457340/1‑68 (MQ=255)

                                                   cGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATcgcc              >  1:724788/1‑68 (MQ=255)

                                                     gCCAGGGCTACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCt           <  1:1088963/69‑1 (MQ=255)

                                                     gCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATcgccgc            <  1:1612537/68‑1 (MQ=255)

                                                     gCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATcgccgc            <  1:2169492/68‑1 (MQ=255)

                                                     gCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCt           <  1:1161667/69‑1 (MQ=255)

                                                     gCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCt           <  1:3007670/69‑1 (MQ=255)

                                                     gCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCt           <  1:500842/69‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:2283442/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:1200869/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:1608864/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:1612658/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:805889/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:1966193/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:77658/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:775523/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:728535/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:3294457/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:618782/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:2467480/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:506493/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:2752026/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:2821113/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:28394/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:3038177/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGTCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:3219201/63‑1 (MQ=255)

                                                         gggCAACCAGAATATGCCAGGCAGCCAGAACACCACCAGCTACGGAACCGAGCAAAATcgccg             <  1:2716555/63‑1 (MQ=255)

                                                              acgaGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGaa  <  1:2147071/69‑1 (MQ=255)

                                                              acgaGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGaa  <  1:2396357/69‑1 (MQ=255)

TGGGAATGTAGATATTGGCAACGACCGCACCACCGTAGGCCAGTGCGCATGCGGCCAGGGCGACGAGGACATGCCAGTCAGCCAGCACACCACCGGCTACGGAACCGAGCAAAATCGCCGCTATGGTAGAA  >  minE/1920344‑1920474

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