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	311,087	G→T	60.9%	H596N (CAT→AAT)	acrB ←	multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	311,087	0	G	T	60.9%	27.1 / 59.6	64	H596N (CAT→AAT)	acrB	multidrug efflux system protein
Reads supporting (aligned to +/- strand): ref base G (21/4); new base T (23/16); total (44/20)
Fisher's exact test for biased strand distribution p-value = 5.26e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCAAAGCCGAAGCCGTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTACGTT  >  minE/311020‑311119

gCAAAGCCGAAGCCGTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATg                                  <  1:823691/68‑1 (MQ=255)

gCAAAGCCGAAGCCGTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATg                                  <  1:2568299/68‑1 (MQ=255)

   aagccgaagccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGtt                              >  1:1924022/1‑69 (MQ=255)

          agccgTTAACGGCGAACACCGAGTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:3109618/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:2108962/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:1169078/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:2136779/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:2461267/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:2648015/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:2676983/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:2730237/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:2774636/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:3048777/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:307403/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:3374087/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:3417124/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:451913/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:452682/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:48193/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:549341/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:580259/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:866652/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:906684/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:1975992/1‑68 (MQ=255)

          agccgTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATTCGTTACCTCa                        >  1:126437/1‑68 (MQ=255)

          agccgATAACGGCGAACACCGACTCAACGTTGTTCTATTCTTTGCTCAGATAGTAATTCGTTACCTCa                        >  1:2106779/1‑68 (MQ=255)

                     gCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGt                               >  1:1319518/1‑50 (MQ=255)

                     gCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGt                               >  1:3261970/1‑50 (MQ=255)

                     gCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGt                               >  1:1953871/1‑50 (MQ=255)

                     gCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGt                               >  1:2341806/1‑50 (MQ=255)

                     gCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGt                               >  1:2052981/1‑50 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGc                  <  1:2125137/56‑1 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGc                  <  1:1549019/56‑1 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGc                  <  1:1619397/56‑1 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTa      >  1:462114/1‑68 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:809778/1‑69 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:773932/1‑69 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:208300/1‑69 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:1039075/1‑69 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:1353359/1‑69 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:1407571/1‑69 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:1459490/1‑69 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:3180752/1‑69 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:2871096/1‑69 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:2164282/1‑69 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:2839009/1‑69 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:1621248/1‑69 (MQ=255)

                            ccGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTATCTGTGTAc     >  1:3420282/1‑69 (MQ=255)

                            ccGACTCAACGGTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTAc     >  1:2854097/1‑69 (MQ=255)

                               aCTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTACGtt  <  1:431832/69‑1 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:1981879/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:2861774/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:1296834/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:2311881/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:2418949/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:2473691/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:1326528/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:2530714/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:1770521/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:1754222/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:14186/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:40179/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:2698969/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:1733324/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:1553748/45‑3 (MQ=255)

                                                 ctttGGTCAGATAGTAATTCGTTACCTCATTGAGCACTTTCtgcg        <  1:1590362/45‑3 (MQ=255)

GCAAAGCCGAAGCCGTTAACGGCGAACACCGACTCAACGTTGTTCTTTTCTTTGGTCAGATAGTAATGCGTTACCTCATTGAGCACTTTCTGTGTACGTT  >  minE/311020‑311119

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