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	650,405	T→C	69.0%	A113A (GCA→GCG)	ssuB ←	alkanesulfonate transporter subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	650,405	0	T	C	69.0%	54.9 / 27.3	61	A113A (GCA→GCG)	ssuB	alkanesulfonate transporter subunit
Reads supporting (aligned to +/- strand): ref base T (5/14); new base C (22/20); total (27/34)
Fisher's exact test for biased strand distribution p-value = 9.40e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGGCAGGCCATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCACGGTAGCA  >  minE/650350‑650472

cGGCAGGCCATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGCATCGCGcc                                                        <  1:3051459/69‑1 (MQ=255)

cGGCAGGCCATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGCATCGCGcc                                                        <  1:1513975/69‑1 (MQ=255)

cGGCAGGCCATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGCATCGCGcc                                                        <  1:1515325/69‑1 (MQ=255)

       ccATTCGCCTTCGCGATTCTCGAGTCCTACCGCAGCCAACGCTCGACGTGCGGc                                                                <  1:207254/54‑1 (MQ=255)

       ccATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGc                                                                <  1:983895/54‑1 (MQ=255)

       ccATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGc                                                                <  1:1990683/54‑1 (MQ=255)

       ccATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGc                                                                <  1:1284225/54‑1 (MQ=255)

       ccATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGc                                                                <  1:2295562/54‑1 (MQ=255)

       ccATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGc                                                                <  1:1504513/54‑1 (MQ=255)

       ccATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGc                                                                <  1:660782/54‑1 (MQ=255)

       ccATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGc                                                                <  1:3077118/54‑1 (MQ=255)

        cATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGc                                                                <  1:821864/53‑1 (MQ=255)

            ccccTGCTCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGCATCGCGCCACTGGCCTTTaa                                            >  1:482636/1‑69 (MQ=255)

            ccccTGCTCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGCATCGCGCCACTGGCCTTTaa                                            >  1:1831013/1‑69 (MQ=255)

                         ctcCAGTCCTACCGCAGCCAACGCTCGACGTGCGGc                                                                <  1:1584320/36‑1 (MQ=255)

                                ccTACCGCAGCCAACGCTCGACGTGCGGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatc                         >  1:2884813/1‑68 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:1162193/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:3333525/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:3266075/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:3142306/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:705267/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:72031/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:2865228/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:2612380/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:918314/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:942503/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:2195471/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:995788/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:1788200/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:1788389/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:203983/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:1744859/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:1197551/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:128780/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:1820514/69‑1 (MQ=255)

                                 cTACCGCAGCCAGAGCCTGACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTatcaa                       <  1:1842351/69‑1 (MQ=255)

                                         gCCAACGCTCGACGTGCGGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGAt               >  1:2096832/1‑69 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTa                                      >  1:168294/2‑37 (MQ=37)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCCCCGATTTCCa          >  1:1195628/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:1510873/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:1568600/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:1613790/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:1633810/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:142985/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:1327516/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:2050066/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:100491/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:3119442/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:2944554/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:2796355/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:2708118/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:1881247/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:2538750/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:2363821/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:2345429/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:1921231/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:2292069/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:2235378/2‑65 (MQ=255)

                                                  tgACGCGCCGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCa          >  1:2165137/2‑65 (MQ=255)

                                                  cGACGTGCGGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCACGGt      >  1:2794582/1‑69 (MQ=255)

                                                      gTGCGGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCACGGTAGCa  <  1:610501/69‑1 (MQ=255)

CGGCAGGCCATTCCCCTGCGCGATTCTCCAGTCCTACCGCAGCCAACGCTCGACGTGCGGCATCGCGCCACTGGCCTTTAAGGCCTAACCCAACGTTATCAATCACCGATTTCCACGGTAGCA  >  minE/650350‑650472

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A