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	1,782,512	C→T	44.1%	I321I (ATC→ATT)	yfjD →	predicted inner membrane protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,782,512	0	C	T	44.1%	16.7 / 51.2	68	I321I (ATC→ATT)	yfjD	predicted inner membrane protein
Reads supporting (aligned to +/- strand): ref base C (13/25); new base T (4/26); total (17/51)
Fisher's exact test for biased strand distribution p-value = 5.53e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.41e-01

TTCACTACGTCGATGTCGCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGAT  >  minE/1782444‑1782572

ttCACTACGTCGATGTCGCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATc                                                              >  1:1880367/1‑69 (MQ=255)

ttCACTACGTCGATGTCGCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATc                                                              >  1:1257957/1‑69 (MQ=255)

ttCACTACGTCGATGTCGCCAACACTTACCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATc                                                              >  1:2624212/1‑69 (MQ=255)

 tCACTACGTCGATGTCGCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCg                                                             >  1:1133936/1‑69 (MQ=255)

      aCGTCGATGTCGCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGc                                                        >  1:2051278/1‑69 (MQ=255)

      aCGTCGATGTCGCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGc                                                        >  1:2948354/1‑69 (MQ=255)

                 gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt                                             >  1:2562557/1‑69 (MQ=255)

                 gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt                                             >  1:2472204/1‑69 (MQ=255)

                 gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt                                             >  1:1856485/1‑69 (MQ=255)

                 gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt                                             >  1:2419969/1‑69 (MQ=255)

                 gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt                                             >  1:516266/1‑69 (MQ=255)

                 gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt                                             >  1:1134505/1‑69 (MQ=255)

                 gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt                                             >  1:1791683/1‑69 (MQ=255)

                 gCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGt                                             >  1:2130351/1‑69 (MQ=255)

                                   ggTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc                           <  1:1213571/69‑1 (MQ=255)

                                   ggTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc                           <  1:1743851/69‑1 (MQ=255)

                                   ggTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc                           <  1:1078091/69‑1 (MQ=255)

                                   ggTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc                           <  1:1583389/69‑1 (MQ=255)

                                   ggTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc                           <  1:279320/69‑1 (MQ=255)

                                   ggTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc                           <  1:2759397/69‑1 (MQ=255)

                                    gTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc                           <  1:1030002/68‑1 (MQ=255)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:2934673/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:2973151/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:2607451/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:3188171/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:2991678/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:3115593/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:2468565/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:3306855/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:3344368/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:347884/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:420631/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:508257/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:521536/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:599400/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:876772/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:923274/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:987933/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:2465051/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:1167556/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:1359320/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:1560564/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:1640703/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:1960414/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:2106743/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:2256603/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATTGATGGCACTGCCAAc                                               <  1:2339948/46‑1 (MQ=39)

                                      cACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCt                         >  1:3404278/1‑68 (MQ=255)

                                             cAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTgg                 <  1:941698/69‑1 (MQ=255)

                                             cAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTgg                 <  1:1449384/69‑1 (MQ=255)

                                             cAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTgg                 <  1:3274276/69‑1 (MQ=255)

                                             cAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTgg                 <  1:2685458/69‑1 (MQ=255)

                                             cAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTgg                 <  1:1583813/69‑1 (MQ=255)

                                               aaaCGACGGTTCTGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGc                           <  1:670005/57‑1 (MQ=255)

                                                         tCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTa                      >  1:3164897/1‑52 (MQ=255)

                                                           ggtggtTATTGATGGCACTGCCAACGTGCGAGAAATTAACAAAGCCTTTAACTGGCATCTACCGGAAg    >  1:1053679/1‑68 (MQ=255)

                                                           ggTGATTATTGATGGCACTGCCAACGTGCGAGAAATTAACAAAGCCTTTAACTGGCATCTACCGGAAg    >  1:2405513/1‑68 (MQ=255)

                                                           ggTGATTATTGATGGCACTGCCAACGTGCGAGAAATTAACAAAGCCTTTAACTGGCATCTACCGGAAg    >  1:71994/1‑68 (MQ=255)

                                                           ggTGATTATTGATGGCACTGCCAACGTGCGAGAAATTAACAAAGCCTTTAACTGGCATCTACCGGAAg    >  1:1481354/1‑68 (MQ=255)

                                                             tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat  <  1:1184052/68‑1 (MQ=255)

                                                             tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat  <  1:2514554/68‑1 (MQ=255)

                                                             tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat  <  1:1530348/68‑1 (MQ=255)

                                                             tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat  <  1:2608647/68‑1 (MQ=255)

                                                             tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat  <  1:559927/68‑1 (MQ=255)

                                                             tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat  <  1:548445/68‑1 (MQ=255)

                                                             tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat  <  1:1412323/68‑1 (MQ=255)

                                                             tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat  <  1:2296053/68‑1 (MQ=255)

                                                             tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat  <  1:1768860/68‑1 (MQ=255)

                                                             tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat  <  1:1807746/68‑1 (MQ=255)

                                                             tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat  <  1:2772620/68‑1 (MQ=255)

                                                             tGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAgat  <  1:2157272/68‑1 (MQ=255)

TTCACTACGTCGATGTCGCCAACACTTGCCGAAGAGGTCACGCCGCAAAACGACGGTTCGGTGATTATCGATGGCACCGCCAACGTGCGGGAAATCAACAAAGCCTTTAACTGGCATCTACCGGAAGAT  >  minE/1782444‑1782572

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A