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	1,914,338	C→T	51.8%	V378V (GTG→GTA)	ptsP ←	fused PEP‑protein phosphotransferase (enzyme I) of PTS system

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,914,338	0	C	T	51.8%	‑1.9 / 73.1	81	V378V (GTG→GTA)	ptsP	fused PEP‑protein phosphotransferase (enzyme I) of PTS system
Reads supporting (aligned to +/- strand): ref base C (12/27); new base T (21/21); total (33/48)
Fisher's exact test for biased strand distribution p-value = 1.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCCGGATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTACCATGAT  >  minE/1914279‑1914397

tCCGGATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAgg                                                     >  1:1425310/1‑68 (MQ=255)

tCCGGATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAgg                                                     >  1:179553/1‑68 (MQ=255)

tCCGGATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAgg                                                     >  1:2342350/1‑68 (MQ=255)

tCCGGATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAgg                                                     >  1:487780/1‑68 (MQ=255)

tCCGGATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAgg                                                     >  1:512899/1‑68 (MQ=255)

    gATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTg                                                  <  1:531935/67‑1 (MQ=255)

    gATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTg                                                  <  1:446821/67‑1 (MQ=255)

    gATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTg                                                  <  1:418726/67‑1 (MQ=255)

    gATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTg                                                  <  1:1533732/67‑1 (MQ=255)

    gATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTg                                                  <  1:2009957/67‑1 (MQ=255)

    gATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTg                                                  <  1:819047/67‑1 (MQ=255)

                 ttCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCAt                                   <  1:563754/69‑1 (MQ=255)

                 ttCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCAt                                   <  1:2476361/69‑1 (MQ=255)

                 ttCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCAt                                   <  1:3271468/69‑1 (MQ=255)

                 ttCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCAt                                   <  1:2554926/69‑1 (MQ=255)

                 ttCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCAt                                   <  1:2492165/69‑1 (MQ=255)

                 ttCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCAt                                   <  1:760248/69‑1 (MQ=255)

                 ttCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCAt                                   <  1:2249118/69‑1 (MQ=255)

                 ttCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCAt                                   <  1:1865159/69‑1 (MQ=255)

                 ttCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCAt                                   <  1:1160491/69‑1 (MQ=255)

                 ttCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCAt                                   <  1:1175943/69‑1 (MQ=255)

                  tCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCAt                                   <  1:20284/68‑1 (MQ=255)

                      cgcgATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACgg                              <  1:604254/69‑1 (MQ=255)

                             gCCATCTACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGAt                       >  1:440339/1‑69 (MQ=255)

                             gCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGAt                       >  1:2855097/1‑69 (MQ=255)

                             gCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGAt                       >  1:1482446/1‑69 (MQ=255)

                             gCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGAt                       >  1:3391775/1‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATcccc                   >  1:3315943/3‑68 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATcccc                   >  1:3259727/3‑68 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATcccc                   >  1:2359381/3‑68 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATcccc                   >  1:1016943/3‑68 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATcccc                   >  1:1799261/3‑68 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:1478724/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:1405008/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:3328164/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:343435/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:2927404/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:517612/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:2512023/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:3370822/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:2412979/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:1081603/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:1892668/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:1916396/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:1961518/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:2221339/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:2438543/3‑69 (MQ=255)

                                  cgaCGATCAGCGTCCGACGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCa                  >  1:2315435/3‑69 (MQ=255)

                                             gTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTAcc       <  1:2663795/69‑1 (MQ=255)

                                             gTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTAcc       <  1:2245738/69‑1 (MQ=255)

                                             gTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTAcc       <  1:2022238/69‑1 (MQ=255)

                                              tCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTAcc       >  1:1226538/1‑68 (MQ=255)

                                              tCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTAcc       >  1:1526735/1‑68 (MQ=255)

                                              tCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTAcc       >  1:216206/1‑68 (MQ=255)

                                                cTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTACCATg    <  1:2631243/69‑1 (MQ=255)

                                                cTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTACCATg    <  1:1807866/69‑1 (MQ=255)

                                                cTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTACCATg    <  1:1721575/69‑1 (MQ=255)

                                                cTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTACCATg    <  1:487107/69‑1 (MQ=255)

                                                cTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTACCATg    <  1:1217682/69‑1 (MQ=255)

                                                 tACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTACCATg    <  1:3365562/68‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGGGCACGTACCATGAt  <  1:2509936/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:1257841/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:675578/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:383692/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:714774/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:2760007/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:365240/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:3372417/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:3062489/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:3016910/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:300669/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:2809585/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:1775170/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:2698171/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:254747/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:2461818/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:2461710/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:240377/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:1565692/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:1714123/69‑1 (MQ=255)

                                                  aCGATGCAGTACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:1736567/69‑1 (MQ=255)

                                                       gcagtaCCGAAGGCTGAATATCCGCGCCCATCACGGTAGGTATCCCCAGCGCACGTACCATGAt  <  1:1022768/64‑1 (MQ=255)

TCCGGATCGACCAGCAATTCACCGCGATAGCCATCAACGATCAGCGTCCTACGATGCAGCACCGAAGGCTGAATATCCGCGCCCATCACGGTAGGGATCCCCAGCGCACGTACCATGAT  >  minE/1914279‑1914397

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