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	1,203,338	G→A	34.9%	L332L (CTG→CTA)	yoaD →	predicted phosphodiesterase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,203,338	0	G	A	34.9%	42.6 / 31.7	60	L332L (CTG→CTA)	yoaD	predicted phosphodiesterase
Reads supporting (aligned to +/- strand): ref base G (11/28); new base A (18/3); total (29/31)
Fisher's exact test for biased strand distribution p-value = 2.82e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-01

GTCAGGGCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTATGTGATGGCAGAAACCATTCGTCAGCGCCATGTTTTCCCGATGAGTAGTCAGTTTCA  >  minE/1203271‑1203403

gTCAGGGCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGa                                                                  <  1:8599/69‑1 (MQ=255)

gTCAGGGCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGa                                                                  <  1:2647592/69‑1 (MQ=255)

gTCAGGGCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGa                                                                  <  1:2519896/69‑1 (MQ=255)

gTCAGGGCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGa                                                                  <  1:1330205/69‑1 (MQ=255)

gTCAGGGCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGa                                                                  <  1:2461119/69‑1 (MQ=255)

gTCAGGGCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGa                                                                  <  1:2210724/69‑1 (MQ=255)

     ggCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGc                                                             <  1:472633/69‑1 (MQ=255)

     ggCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGc                                                             <  1:1451656/69‑1 (MQ=255)

     ggCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGc                                                             <  1:1486655/69‑1 (MQ=255)

     ggCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGc                                                             <  1:1804637/69‑1 (MQ=255)

     ggCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGc                                                             <  1:1761461/69‑1 (MQ=255)

      gCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCt                                                            >  1:2865801/1‑69 (MQ=255)

      gCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCt                                                            >  1:1916848/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGGGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:1031366/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTa                                                           >  1:2914458/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:567384/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:466411/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:3380338/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:3341777/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:547940/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:3153994/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:3141139/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:172673/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:3111970/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:3068019/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:2982169/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:2661839/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:2577775/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:1599484/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:2051392/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:2552065/1‑69 (MQ=255)

       cTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTAACCCGCTa                                                           >  1:2565536/1‑69 (MQ=255)

            tttCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTAtgt                                                        <  1:1100991/67‑1 (MQ=255)

            tttCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTAtgt                                                        <  1:107024/67‑1 (MQ=255)

            tttCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTAtgt                                                        <  1:1245271/67‑1 (MQ=255)

            tttCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTAtgt                                                        <  1:1041227/67‑1 (MQ=255)

            tttCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTAtgt                                                        <  1:2244787/67‑1 (MQ=255)

            tttCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTAtgt                                                        <  1:3125122/67‑1 (MQ=255)

            tttCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTAtgt                                                        <  1:396259/67‑1 (MQ=255)

            tttCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTAtgt                                                        <  1:2803129/67‑1 (MQ=255)

            tttCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTAtgt                                                        <  1:488022/67‑1 (MQ=255)

            tttCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTAtgt                                                        <  1:145037/67‑1 (MQ=255)

              tCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTAtgt                                                        <  1:372418/65‑1 (MQ=255)

              tCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTATGTGAt                                                     >  1:83201/1‑68 (MQ=255)

              tCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTATGTGAt                                                     >  1:1019422/1‑68 (MQ=255)

              tCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTATGTGAt                                                     >  1:2904870/1‑68 (MQ=255)

              tCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTATGTGAt                                                     >  1:134321/1‑68 (MQ=255)

                                ccTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTATGTGATGGCAGAAACCATTCGTCa                                   >  1:679424/1‑68 (MQ=255)

                                ccTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTATGTGATGGCAGAAACCATTCGTCAg                                  >  1:3113062/1‑69 (MQ=255)

                                ccTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTATGTGATGGCAGAAACCATTCGTCAg                                  >  1:44156/1‑69 (MQ=255)

                                ccTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTATGTGATGGCAGAAACCATTCGTCAg                                  >  1:1983031/1‑69 (MQ=255)

                                    tCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTAtgt                                                        <  1:3323248/43‑1 (MQ=255)

                                              aCATCATTTAATTGTGCCACTGACCCGCTATGTGATGGCAGAAACCATTCGTTAGCGCCATGTTTTccc                    <  1:921329/69‑1 (MQ=255)

                                              aCATCATTTAATTGTGCCACTGACCCGCTATGTGATGGCAGAAACCATTCGTCAGCGCCATGTTTTccc                    <  1:2902530/69‑1 (MQ=255)

                                              aCATCATTTAATTGTGCCACTGACCCGCTATGTGATGGCAGAAACCATTCGTCAGCGCCATGTTTTccc                    <  1:576192/69‑1 (MQ=255)

                                               catcatTTAATTGTGCCACTAACCCGCTATGTGATGGCAGAAACCATTCGTCAGCGCCATGTTTTccca                   <  1:1372691/69‑2 (MQ=255)

                                               catcatTTAATTGTGCCACTAACCCGCTATGTGATGGCAGAAACCATTCGTCAGCGCCATGTTTTccca                   <  1:910097/69‑2 (MQ=255)

                                                atcatTTAATTGTGCCACTAACCCGCTATGTGATGGCAGAAACCATTCGTCAGCGCCATGTTTTccca                   <  1:426959/68‑2 (MQ=255)

                                                   atTTAATTGTGCCACTGACCCGCTATGTGATGGCAGAAACCATTCGTCAGCGCCATGTTTTCCCGATGa               <  1:3414336/69‑1 (MQ=255)

                                                                aCTGACCCGCTATGTGATGGCAGAAACCATTCGTCAGCGCCATGTTTTCCCGATGAGTAGTCAGTTTCa  <  1:2107865/69‑1 (MQ=255)

GTCAGGGCTGGATTTCACCGGATGTGTTTATTCCTATCGCGGAAGAACATCATTTAATTGTGCCACTGACCCGCTATGTGATGGCAGAAACCATTCGTCAGCGCCATGTTTTCCCGATGAGTAGTCAGTTTCA  >  minE/1203271‑1203403

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