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	1,793,884	A→G	56.5%	L250L (TTA→TTG)	gabP →	gamma‑aminobutyrate transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,793,884	0	A	G	56.5%	16.3 / 45.4	62	L250L (TTA→TTG)	gabP	gamma‑aminobutyrate transporter
Reads supporting (aligned to +/- strand): ref base A (20/7); new base G (27/8); total (47/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

CCGGAAAAACATATTGTCCGCGCCACCAACTCGGTTATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAATATGCCCGGACTAAAAGCCGTC  >  minE/1793822‑1793944

ccGGAAAAACATATTGACCGCGCCACCAACTCGGTTATCTGGCGTATTTCTATCTTCTATTTATGTTCt                                                        >  1:1706613/1‑69 (MQ=255)

    aaaaaCATATTGTCCGCGCCACCAACTCGGTTATCTGGCGTATCTCTATTTTCTATTTGTGTTCTAttt                                                    <  1:2652593/69‑1 (MQ=255)

    aaaaaCATATTGTCCGCGCCACCAACTCGGTTATCTGGCGTATCTCTATTTTCTATTTGTGTTCTAttt                                                    <  1:185291/69‑1 (MQ=255)

    aaaaaCATATTGTCCGCGCCACCAACTCGGTTATCTGGCGTATCTCTATTTTCTATTTGTGTTCTAttt                                                    <  1:3242604/69‑1 (MQ=255)

    aaaaaCATATTGTCCGCGCCACCAACTCGGTTATCTGGCGTATCTCTATTTTCTATTTGTGTTCTAttt                                                    <  1:2897817/69‑1 (MQ=255)

    aaaaaCATATTGTCCGCGCCACCAACTCGGTTATCTGGCGTATCTCTATTTTCTATTTGTGTTCTAttt                                                    <  1:2222281/69‑1 (MQ=255)

    aaaaaCATATTGTCCGCGCCACCAACTCGGTTATCTGGCGTATCTCTATTTTCTATTTGTGTTCTAttt                                                    <  1:2786184/69‑1 (MQ=255)

    aaaaaCATATTGTCCGCGCCACCAACTCGGTTATCTGGCGTATCTCTATTTTCTATTTGTGTTCTAttt                                                    <  1:1187310/69‑1 (MQ=255)

    aaaaaCATATTGTCCGCGCCACCAACTCGGTTATCTGGCGTATCTCTATTTTCTATTTGTGTTCTAttt                                                    <  1:2771632/69‑1 (MQ=255)

                           aaCTCGGTTATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCg                             >  1:628850/1‑69 (MQ=255)

                           aaCTCGGTTATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCg                             >  1:799859/1‑69 (MQ=255)

                           aaCTCGGTTATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCg                             >  1:2534380/1‑69 (MQ=255)

                           aaCTCGGTTATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCg                             >  1:1769849/1‑69 (MQ=255)

                           aaCTCGGTTATCTGGCGTATTTCTATATTCTATTTATGTTCTATTTTTGTcgtcgt                                          >  1:165012/1‑56 (MQ=255)

                                  ttATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGaa                        <  1:1040027/67‑1 (MQ=255)

                                  ttATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGaa                        <  1:3036435/67‑1 (MQ=255)

                                  ttATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAata                      <  1:2298867/69‑1 (MQ=255)

                                  ttATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAata                      <  1:1685975/69‑1 (MQ=255)

                                   tATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGaa                        >  1:186815/1‑66 (MQ=255)

                                   tATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGaa                        >  1:1105606/1‑66 (MQ=255)

                                   tATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGaa                        >  1:1793133/1‑66 (MQ=255)

                                   tATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGaa                        >  1:1672850/1‑66 (MQ=255)

                                   tATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGaa                        >  1:15352/1‑66 (MQ=255)

                                       tGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAATATGcc                  >  1:3393629/1‑68 (MQ=255)

                                       tGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAATATGcc                  >  1:2689591/1‑68 (MQ=255)

                                                tctattttctatttGTGTTCTATTTTTGTCGTTGTTGCa                                      >  1:1118394/1‑39 (MQ=25)

                                                tctattttctatttGTGTTCTATTTTTGTCGTTGTGGCa                                      >  1:1834504/1‑39 (MQ=37)

                                                tctattttctatttGTGTTCTATTTTTGTCGTTGTGGCa                                      >  1:1149135/1‑39 (MQ=37)

                                                tctattttctatttGTGTTCTATTTTTGTCGTTGTGGCa                                      >  1:1220562/1‑39 (MQ=37)

                                                tctattttctatttGTGTTCTATTTTTGTCGTTGTGGCa                                      >  1:234945/1‑39 (MQ=37)

                                                tctattttctatttGTGTTCTATTTTTGTCGTTGTGGCa                                      >  1:797251/1‑39 (MQ=37)

                                                tctattttctatttGTGTTCTATTTTTGTCGTTGTGGCa                                      >  1:1413555/1‑39 (MQ=37)

                                                tctattttctatttGTGTTCTATTTTTGTCGTTGTGGCa                                      >  1:648896/1‑39 (MQ=37)

                                                tctattttctatttGTGTTCTATTTTTGTCGTTGTGGCa                                      >  1:2150904/1‑39 (MQ=37)

                                                tctattttctatttGTGTTCTATTTTTGTCGTTGTGGCa                                      >  1:2150645/1‑39 (MQ=37)

                                                tctattttctatttGTGTTCTATTTTTGTCGTTGTGGCa                                      >  1:346375/1‑39 (MQ=37)

                                                tctattttctatttGTGTTCTATTTTTGTCGTTGTGGCa                                      >  1:1740033/1‑39 (MQ=37)

                                                  tATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTaa                                  <  1:2790792/41‑1 (MQ=255)

                                                  tATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTaa                                  <  1:2247031/41‑1 (MQ=255)

                                                  tATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTaa                                  <  1:12373/41‑1 (MQ=255)

                                                      ttctATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAATATGCCCGGACTAAAAg       >  1:1498268/1‑64 (MQ=255)

                                                      ttctATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAATATGCCCGGACTAAAAGCCGTc  >  1:920187/1‑69 (MQ=255)

                                                      ttctATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAATATGCCCGGACTAAAAGCCGTc  >  1:1137310/1‑69 (MQ=255)

                                                      ttctATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAATATGCCCGGACTAAAAGCCGTc  >  1:2216360/1‑69 (MQ=255)

                                                      ttctATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAATATGCCCGGACTAAAAGCCGTc  >  1:292643/1‑69 (MQ=255)

                                                      ttctATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAATATGCCCGGACTAAAAGCCGTc  >  1:1563273/1‑69 (MQ=255)

                                                      ttctATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAATATGCCCGGACTAAAAGCCGTc  >  1:3321347/1‑69 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCTAGGGCTGAAAg       >  1:3104130/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:3131537/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:684205/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:1460998/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:1795484/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:1855380/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:3240411/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:2358676/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:309162/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:3082812/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:1958803/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:3014029/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:286556/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:2219276/1‑61 (MQ=255)

                                                         tATTTGTGTTCTATTTTTGTCGTTGTGGCATTAATCCCGTGGAATATGCCAGGGCTGAAAg       >  1:2350424/1‑61 (MQ=255)

CCGGAAAAACATATTGTCCGCGCCACCAACTCGGTTATCTGGCGTATTTCTATCTTCTATTTATGTTCTATTTTTGTCGTCGTGGCATTAATTCCGTGGAATATGCCCGGACTAAAAGCCGTC  >  minE/1793822‑1793944

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