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	274,364	G→A	46.3%	L258L (CTA→TTA)	yajR ←	predicted transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	274,364	0	G	A	46.3%	5.4 / 42.5	54	L258L (CTA→TTA)	yajR	predicted transporter
Reads supporting (aligned to +/- strand): ref base G (7/22); new base A (13/12); total (20/34)
Fisher's exact test for biased strand distribution p-value = 4.91e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.17e-01

GCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGCAT  >  minE/274301‑274414

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAACAtcg                                               >  1:2895864/1‑67 (MQ=255)

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAACAtcg                                               >  1:2518016/1‑67 (MQ=255)

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAACAtcg                                               >  1:2529696/1‑67 (MQ=255)

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAACAtcg                                               >  1:2353996/1‑67 (MQ=255)

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAACAtcg                                               >  1:2249752/1‑67 (MQ=255)

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAACAtcg                                               >  1:2708949/1‑67 (MQ=255)

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAACAtcg                                               >  1:28810/1‑67 (MQ=255)

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAACAtcg                                               >  1:1562966/1‑67 (MQ=255)

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAACAtcg                                               >  1:3335074/1‑67 (MQ=255)

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAACAtcg                                               >  1:814241/1‑67 (MQ=255)

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAACAtc                                                >  1:1626276/1‑67 (MQ=255)

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACAGAGCCAAAGGCGATTAACAtcg                                               >  1:2188719/1‑67 (MQ=255)

gCTTCATTTTGCGCTTAACTTCAGCGTAGATAATCAAAGGCACGACCGAGCCAAAGGCGATTAACAtc                                                >  1:2212813/1‑67 (MQ=255)

  ttCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGt                                              >  1:1032273/1‑68 (MQ=255)

  ttCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTc                                             >  1:2959308/1‑69 (MQ=255)

  ttCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTc                                             >  1:1053713/1‑69 (MQ=255)

  ttCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTc                                             >  1:1097619/1‑69 (MQ=255)

  ttCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTc                                             >  1:2825421/1‑69 (MQ=255)

        ttGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGa                                       <  1:2860361/69‑1 (MQ=255)

        ttGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGa                                       <  1:1340218/69‑1 (MQ=255)

        ttGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGa                                       <  1:57045/69‑1 (MQ=255)

        ttGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGa                                       <  1:3258008/69‑1 (MQ=255)

            gcTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAg                                    <  1:1616852/68‑1 (MQ=255)

                    tCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCa                            >  1:492589/1‑68 (MQ=255)

                             aTAATGAAAGGCACGACCGAGCCAAAGGCGATTTGCATTGTCGCCAGATAGCCCTTCCAGTGTTCAgcc                  >  1:2440841/1‑69 (MQ=255)

                                      ggCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAAc         <  1:2532855/69‑1 (MQ=255)

                                          cGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTg     <  1:856434/69‑1 (MQ=255)

                                          cGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTg     <  1:3414369/69‑1 (MQ=255)

                                          cGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTg     <  1:1384152/69‑1 (MQ=255)

                                          cGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTg     <  1:1944602/69‑1 (MQ=255)

                                          cGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTg     <  1:2639095/69‑1 (MQ=255)

                                           gACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTTTTCAGCCGCCGGGAACCCTGc    <  1:724778/69‑1 (MQ=255)

                                           gACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTg     <  1:2069039/68‑1 (MQ=255)

                                           gACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTg     <  1:1267382/68‑1 (MQ=255)

                                           gACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTg     <  1:2897285/68‑1 (MQ=255)

                                           gACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGc    <  1:1934353/69‑1 (MQ=255)

                                           gACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGc    <  1:1813467/69‑1 (MQ=255)

                                           gACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGc    <  1:1558832/69‑1 (MQ=255)

                                           gACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGc    <  1:490192/69‑1 (MQ=255)

                                           gACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGc    <  1:1544984/69‑1 (MQ=255)

                                           gACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGc    <  1:380898/69‑1 (MQ=255)

                                           gACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGc    <  1:3400843/69‑1 (MQ=255)

                                             ccGAGCCAAAGGCGATTAACATCGTTGCCAGGTAGACCTTCCAGTGTTCAGCCGCCGGTAACCCCGCAt  <  1:712195/69‑1 (MQ=255)

                                             ccGAGCCAAAGGCGATTAACATCGTTGCCAGGTAGACCTTCCAGTGTTCAGCCGCCGGTAACCCCGCAt  <  1:1274138/69‑1 (MQ=255)

                                             ccGAGCCAAAGGCGATTAACATCGTTGCCAGGTAGACCTTCCAGTGTTCAGCCGCCGGTAACCCCGCAt  <  1:1188240/69‑1 (MQ=255)

                                             ccGAGCCAAAGGCGATTAACATCGTTGCCAGGTAGACCTTCCAGTGTTCAGCCGCCGGTAACCCCGCAt  <  1:2977611/69‑1 (MQ=255)

                                             ccGAGCCAAAGGCGATTAACATCGTTGCCAGGTAGACCTTCCAGTGTTCAGCCGCCGGTAACCCCGCAt  <  1:2431419/69‑1 (MQ=255)

                                             ccGAGCCAAAGGCGATTAACATCGTTGCCAGGTAGACCTTCCAGTGTTCAGCCGCCGGTAACCCCGCAt  <  1:2881795/69‑1 (MQ=255)

                                             ccGAGCCAAAGGCGATTAACATCGTTGCCAGGTAGACCTTCCAGTGTTCAGCCGCCGGTAACCCCGCAt  <  1:1871157/69‑1 (MQ=255)

                                             ccGAGCCAAAGGCGATTAACATCGTTGCCAGGTAGACCTTCCAGTGTTCAGCCGCCGGTAACCCCGCAt  <  1:2717460/69‑1 (MQ=255)

                                             ccGAGCCAAAGGCGATTAACATCGTTGCCAGGTAGACCTTCCAGTGTTCAGCCGCCGGTAACCCCGCAt  <  1:2626387/69‑1 (MQ=255)

                                             ccGAGCCAAAGGCGATTAACATCGTTGCCAGGTAGACCTTCCAGTGTTCAGCCGCCGGTAACCCCGCAt  <  1:2588724/69‑1 (MQ=255)

                                             ccGAGCCAAAGGCGATTAACATCGTTGCCAGGTAGACCTTCCAGTGTTCAGCCGCCGGTAACCCCGCAt  <  1:2150457/69‑1 (MQ=255)

                                               gAGCCAAAGGCGATTAACATCGTTGCCAGGTAGACCTTCCAGTGTTCAGCCGCCGGTAACCCCGCAt  <  1:330532/67‑1 (MQ=255)

GCTTCATTTTGCGCTTAACTTCAGCGTAGATAATGAAAGGCACGACCGAGCCAAAGGCGATTAGCATTGTCGCCAGATAGACCTTCCAGTGTTCAGCCGCCGGGAACCCTGCAT  >  minE/274301‑274414

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