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	1,944,009	T→C	32.4%	Y360Y (TAT→TAC)	bglA →	6‑phospho‑beta‑glucosidase A

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,944,009	0	T	C	32.4%	61.1 / 39.2	77	Y360Y (TAT→TAC)	bglA	6‑phospho‑beta‑glucosidase A
Reads supporting (aligned to +/- strand): ref base T (47/5); new base C (12/13); total (59/18)
Fisher's exact test for biased strand distribution p-value = 9.05e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCAAACCCGTATGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCTT  >  minE/1943946‑1944076

aCCAAACCCGTATGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACt                                                                <  1:1074441/69‑1 (MQ=255)

aCCAAACCCGTATGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACt                                                                <  1:569488/69‑1 (MQ=255)

aCCAAACCCGTATGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACt                                                                <  1:1366614/69‑1 (MQ=255)

      tccGTATGTTAAAGCGTCTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGa                                                          <  1:992903/68‑1 (MQ=255)

      tccGTATGTTAAAGCGTCTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGa                                                          <  1:2104768/68‑1 (MQ=255)

      tccGTATGTTAAAGCGTCTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGa                                                          <  1:2073786/68‑1 (MQ=255)

      tccGTATGTTAAAGCGTCTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGa                                                          <  1:2054752/68‑1 (MQ=255)

      tccGTATGTTAAAGCGTCTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGa                                                          <  1:2187372/68‑1 (MQ=255)

      tccGTATGTTAAAGCGTCTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGa                                                          <  1:2677372/68‑1 (MQ=255)

      tccGTATGTTAAAGCGTCTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGa                                                          <  1:3239119/68‑1 (MQ=255)

      tccGTATGTTAAAGCGTCTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGa                                                          <  1:1449904/68‑1 (MQ=255)

      tccGTATGTTAAAGCGTCTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGa                                                          <  1:438135/68‑1 (MQ=255)

      tccGTATGTTAAAGCGTCTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGa                                                          <  1:847254/68‑1 (MQ=255)

      tccGTATGTTAAAGCGTCTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGa                                                          <  1:1199612/68‑1 (MQ=255)

      tccGTATGTTAAAGCGTCTGACTGGGGCTGGCAGATTGATCCGGTTGGGCTGCGCTACGCACTTTGCGa                                                          <  1:2981268/68‑1 (MQ=255)

      cccGTATGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACt                                                                <  1:2100564/63‑1 (MQ=255)

            tGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGt                                                     >  1:44690/1‑68 (MQ=255)

            tGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGt                                                     >  1:1910316/1‑68 (MQ=255)

            tGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGt                                                     >  1:2524906/1‑68 (MQ=255)

            tGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGt                                                     >  1:2624762/1‑68 (MQ=255)

            tGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGt                                                     >  1:3002375/1‑68 (MQ=255)

            tGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGt                                                     >  1:483129/1‑68 (MQ=255)

            tGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGt                                                     >  1:1339520/1‑68 (MQ=255)

              ttAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGTATg                                                  >  1:3253312/1‑69 (MQ=255)

              ttAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGTATg                                                  >  1:83558/1‑69 (MQ=255)

                       cTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGc                                                                   >  1:2173487/1‑43 (MQ=37)

                       cTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGAGCTGTATGAGCGtt                                            >  1:1603640/1‑66 (MQ=255)

                       cTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGAGCTGTATGAGCGtt                                            >  1:3036607/1‑66 (MQ=255)

                       cTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGAGCTGTATGAGCGtt                                            >  1:1734114/1‑66 (MQ=255)

                       cTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGAGCTGTATGAGCGtt                                            >  1:579077/1‑66 (MQ=255)

                       cTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGAGCTGTATGAGCGtt                                            >  1:2576541/1‑66 (MQ=255)

                       cTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGAGCTGTATGAGCGtt                                            >  1:2379569/1‑66 (MQ=255)

                       cTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGAGCTGTATGAGCGtt                                            >  1:2188459/1‑66 (MQ=255)

                       cTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGAGCTGTATGAGCGtt                                            >  1:1336362/1‑66 (MQ=255)

                       cTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGAGCTGTATGAGCGtt                                            >  1:1084922/1‑66 (MQ=255)

                       cTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGAGCTGTATGAGCGt                                             >  1:21974/1‑65 (MQ=255)

                       cTGACTGGGGCTGGCAGATTGATCCGGTTGGTCTGCGCTACGCAATTTGCGAGCTGTATGAGCGtt                                            >  1:2189412/1‑66 (MQ=255)

                                gCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCg                                 >  1:201986/1‑68 (MQ=255)

                                gCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGc                                >  1:1923780/1‑69 (MQ=255)

                                gCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGc                                >  1:1244490/1‑69 (MQ=255)

                                gCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGc                                >  1:3416042/1‑69 (MQ=255)

                                gCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGc                                >  1:2699655/1‑69 (MQ=255)

                                    gCAGATTGATCCGGTTGGTCTGCGCTACGCACTTTGCGa                                                          <  1:1036783/39‑1 (MQ=37)

                                         ttGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTg                       >  1:2374846/1‑69 (MQ=255)

                                                   aGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACgg             >  1:587986/1‑69 (MQ=255)

                                                   aGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACgg             >  1:1399990/1‑69 (MQ=255)

                                                   aGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACgg             >  1:280915/1‑69 (MQ=255)

                                                   aGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACgg             >  1:1892193/1‑69 (MQ=255)

                                                   aGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACgg             >  1:2058971/1‑69 (MQ=255)

                                                   aGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACgg             >  1:2408483/1‑69 (MQ=255)

                                                    ggTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACg              >  1:628243/1‑67 (MQ=255)

                                                    ggTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGt            >  1:938634/1‑69 (MQ=255)

                                                    ggTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGt            >  1:593712/1‑69 (MQ=255)

                                                    ggTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGt            >  1:802459/1‑69 (MQ=255)

                                                    ggTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGt            >  1:1890862/1‑69 (MQ=255)

                                                    ggTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGt            >  1:3373473/1‑69 (MQ=255)

                                                    ggTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGt            >  1:3357607/1‑69 (MQ=255)

                                                    ggTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGt            >  1:3034656/1‑69 (MQ=255)

                                                    ggTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGt            >  1:1602428/1‑69 (MQ=255)

                                                    ggTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGt            >  1:918949/1‑69 (MQ=255)

                                                          cgcTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGgc      >  1:1487507/1‑69 (MQ=255)

                                                          cgcTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGgc      >  1:3185332/1‑69 (MQ=255)

                                                          cgcTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGgc      >  1:3162673/1‑69 (MQ=255)

                                                          cgcTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGgc      >  1:1088393/1‑69 (MQ=255)

                                                          cgcTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGgc      >  1:778376/1‑69 (MQ=255)

                                                          cgcTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGgc      >  1:188723/1‑69 (MQ=255)

                                                            cTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGgc      <  1:181073/67‑1 (MQ=255)

                                                             tATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACgg             >  1:3353239/1‑59 (MQ=255)

                                                             tATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCt   >  1:1052229/1‑69 (MQ=255)

                                                             tATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCt   >  1:1177098/1‑69 (MQ=255)

                                                             tATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCt   >  1:1214577/1‑69 (MQ=255)

                                                             tATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCt   >  1:485289/1‑69 (MQ=255)

                                                             tATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCt   >  1:1441158/1‑69 (MQ=255)

                                                             tATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCt   >  1:1558462/1‑69 (MQ=255)

                                                             tATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCt   >  1:1669835/1‑69 (MQ=255)

                                                             tATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCt   >  1:170470/1‑69 (MQ=255)

                                                             tATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCt   >  1:2566535/1‑69 (MQ=255)

                                                               tGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCtt  >  1:545078/1‑68 (MQ=255)

                                                               tGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCtt  >  1:1261751/1‑68 (MQ=255)

                                                               tGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCtt  >  1:1464002/1‑68 (MQ=255)

ACCAAACCCGTATGTTAAAGCATCTGACTGGGGCTGGCAGATTGATCCAGTAGGTCTGCGCTATGCACTTTGCGAACTGTATGAGCGTTATCAGAGGCCGCTGTTTATTGTCGAAAACGGTTTTGGCGCTT  >  minE/1943946‑1944076

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