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	2,785,788	A→C	32.9%	V79V (GTA→GTC)	yjbC →	23S rRNA pseudouridine synthase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,785,788	0	A	C	32.9%	58.0 / 54.8	73	V79V (GTA→GTC)	yjbC	23S rRNA pseudouridine synthase
Reads supporting (aligned to +/- strand): ref base A (24/25); new base C (21/3); total (45/28)
Fisher's exact test for biased strand distribution p-value = 1.83e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.17e-01

TTGATTGAACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCAAACGCGTGT  >  minE/2785723‑2785852

ttgattgaACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGc                                                               <  1:1584315/69‑1 (MQ=255)

  gattgaACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTa                                                                  >  1:426872/1‑64 (MQ=255)

  gattgaACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTa                                                                  >  1:1521659/1‑64 (MQ=255)

  gattgaACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGcac                                                             <  1:2227778/69‑1 (MQ=255)

  gattgaACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGcac                                                             <  1:2323389/69‑1 (MQ=255)

  gattgaACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGcac                                                             <  1:1767847/69‑1 (MQ=255)

  gattgaACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGcac                                                             <  1:2562653/69‑1 (MQ=255)

      gaACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGcaccac                                                          >  1:3351117/1‑68 (MQ=255)

      gaACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGcaccac                                                          >  1:1214044/1‑68 (MQ=255)

      gaACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGcaccac                                                          >  1:942451/1‑68 (MQ=255)

      gaACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGcaccac                                                          >  1:2608818/1‑68 (MQ=255)

         ccTCGTGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      <  1:1739771/69‑1 (MQ=255)

         ccTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      <  1:159812/69‑1 (MQ=255)

         ccTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      <  1:2616796/69‑1 (MQ=255)

         ccTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      <  1:1687823/69‑1 (MQ=255)

         ccTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      <  1:2681996/69‑1 (MQ=255)

         ccTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      <  1:2830762/69‑1 (MQ=255)

         ccTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      <  1:3017630/69‑1 (MQ=255)

          cTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      <  1:1290272/68‑1 (MQ=255)

                            tGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGcac                                                             <  1:2862656/43‑1 (MQ=255)

                            tGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAAc                                    <  1:3275101/68‑1 (MQ=255)

                                   tATCGCCCTGAACAAGCCCGTTGGTATTGTAAGcaccac                                                          >  1:2393826/1‑39 (MQ=255)

                                   tATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      <  1:1663428/43‑1 (MQ=255)

                                   tATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTc                              >  1:55721/1‑67 (MQ=255)

                                   tATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTc                              >  1:370266/1‑67 (MQ=255)

                                   tATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTc                              >  1:1917950/1‑67 (MQ=255)

                                    aTCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      >  1:606010/1‑42 (MQ=255)

                                    aTCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      >  1:3430934/1‑42 (MQ=255)

                                    aTCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      >  1:847955/1‑42 (MQ=255)

                                    aTCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      >  1:1747717/1‑42 (MQ=255)

                                    aTCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      >  1:1445491/1‑42 (MQ=255)

                                    aTCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      >  1:127114/1‑42 (MQ=255)

                                    aTCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      >  1:438857/1‑42 (MQ=255)

                                    aTCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      >  1:1233715/1‑42 (MQ=255)

                                    aTCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      >  1:2094155/1‑42 (MQ=255)

                                    aTCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGAt                           >  1:1213961/1‑69 (MQ=255)

                                    aTCGACCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGaa                                                      >  1:2905320/1‑42 (MQ=255)

                                          cTGAACAAGCCCGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGtt                     <  1:2446178/69‑1 (MQ=255)

                                          cTGAACAAGCCCGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGtt                     <  1:2714635/69‑1 (MQ=255)

                                             aaCAAGCCGGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTa                    <  1:1690489/67‑1 (MQ=255)

                                               cAAGCCCGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAAc                  <  1:1899039/67‑1 (MQ=255)

                                                    ccGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGct           <  1:349813/69‑2 (MQ=255)

                                                    ccGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCa           <  1:1988097/69‑1 (MQ=255)

                                                    ccGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCa           <  1:595345/69‑1 (MQ=255)

                                                    ccGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCa           <  1:2163236/69‑1 (MQ=255)

                                                    ccGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCa           <  1:498957/69‑1 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:87665/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:369363/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:785975/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:2468416/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:961727/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:3039264/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:1832416/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:2677096/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:2673105/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:1091253/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:2450322/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:2362168/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:1836584/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:1904312/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:2109430/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:1571065/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:1977943/1‑69 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCa           >  1:1739530/1‑68 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCa           >  1:73886/1‑68 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCa           >  1:578133/1‑68 (MQ=255)

                                                     cGTCGGTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCa           >  1:424997/1‑68 (MQ=255)

                                                     cGTCGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCaa          >  1:3281411/1‑69 (MQ=255)

                                                         ggTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCAAAcgc      <  1:592724/69‑1 (MQ=255)

                                                         ggTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCAAAcgc      <  1:478619/69‑1 (MQ=255)

                                                         ggTATTGTCAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCAAAcgc      <  1:144632/69‑1 (MQ=255)

                                                             ttGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCAAACGCgtgt  >  1:1134124/1‑69 (MQ=255)

                                                             ttGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCAAACGCgtgt  >  1:542488/1‑69 (MQ=255)

                                                             ttGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCAAACGCgtgt  >  1:2311684/1‑69 (MQ=255)

                                                             ttGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCAAACGCgtgt  >  1:3369731/1‑69 (MQ=255)

TTGATTGAACCTCGGGAAGCCGAAGATTTGGTACTTATCGCCCTGAACAAGCCCGTTGGTATTGTAAGCACCACCGAAGATGGCGAGCGCGATAACATTGTCGATTTCGTTAACCACAGCAAACGCGTGT  >  minE/2785723‑2785852

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