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	1,793,548	T→C	58.8%	T138T (ACT→ACC)	gabP →	gamma‑aminobutyrate transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,793,548	0	T	C	58.8%	25.0 / 42.3	63	T138T (ACT→ACC)	gabP	gamma‑aminobutyrate transporter
Reads supporting (aligned to +/- strand): ref base T (18/8); new base C (11/26); total (29/34)
Fisher's exact test for biased strand distribution p-value = 2.45e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

CCTGCACTCATGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTC  >  minE/1793482‑1793614

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:3005730/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:2295442/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:2326674/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:2256869/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:2634725/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:2723863/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:2808281/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:3069086/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:1629718/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:1622870/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:3107505/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:3150833/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:3210266/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:1264775/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:622797/69‑1 (MQ=255)

ccTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTCTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:2631195/69‑1 (MQ=255)

ccTGCACTCATGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACt                                                                    >  1:794851/1‑67 (MQ=255)

 cTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:3156950/68‑1 (MQ=255)

 cTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:2550927/68‑1 (MQ=255)

 cTGCACTCGTGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACCgg                                                                  <  1:2345185/68‑1 (MQ=255)

      cTCATGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTaa                                                            <  1:1556486/69‑1 (MQ=255)

      cTCATGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTaa                                                            <  1:275204/69‑1 (MQ=255)

      cTCATGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTaa                                                            <  1:2459209/69‑1 (MQ=255)

      cTCATGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTaa                                                            <  1:2241429/69‑1 (MQ=255)

       tCATGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTaa                                                            <  1:1161733/68‑1 (MQ=255)

          tGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTaa                                                            <  1:859818/65‑1 (MQ=255)

                         cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                         >  1:2318302/1‑69 (MQ=255)

                         cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                         >  1:3358737/1‑69 (MQ=255)

                         cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                         >  1:3338497/1‑69 (MQ=255)

                         cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                         >  1:1431249/1‑69 (MQ=255)

                         cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                         >  1:1500965/1‑69 (MQ=255)

                         cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                         >  1:1734435/1‑69 (MQ=255)

                         cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                         >  1:2751937/1‑69 (MQ=255)

                         cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                         >  1:2584576/1‑69 (MQ=255)

                         cccATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAAc                                         >  1:2463978/1‑69 (MQ=255)

                               tGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACgg                                    >  1:3047236/1‑68 (MQ=255)

                                    aTTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTaaa                                            >  1:1724588/1‑55 (MQ=255)

                                        tCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGa                           >  1:2270643/1‑68 (MQ=255)

                                        tCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGa                           >  1:1241837/1‑68 (MQ=255)

                                        tCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAg                          >  1:1788878/1‑69 (MQ=255)

                                        tCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAg                          >  1:2542712/1‑69 (MQ=255)

                                        tCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAg                          >  1:569431/1‑69 (MQ=255)

                                        tCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAg                          >  1:1419960/1‑69 (MQ=255)

                                                   tACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCtggctggc               <  1:1667118/69‑1 (MQ=255)

                                                    aCCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGgcg              >  1:1836693/1‑69 (MQ=255)

                                                         cGCCTTAACCGG‑AGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt        <  1:644270/69‑2 (MQ=255)

                                                          gCCTTAATCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg         >  1:3101452/1‑68 (MQ=255)

                                                          gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAAt                               >  1:1069886/1‑46 (MQ=38)

                                                          gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTTGCTGGCGCtgtg         >  1:2821661/1‑68 (MQ=255)

                                                          gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtttg         >  1:211517/1‑68 (MQ=255)

                                                          gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg         >  1:517412/1‑68 (MQ=255)

                                                          gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg         >  1:353485/1‑68 (MQ=255)

                                                          gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg         >  1:2268817/1‑68 (MQ=255)

                                                          gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg         >  1:554738/1‑68 (MQ=255)

                                                          gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg         >  1:1595027/1‑68 (MQ=255)

                                                          gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg         >  1:2554604/1‑68 (MQ=255)

                                                          gCCTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtg         >  1:200746/1‑68 (MQ=255)

                                                            cTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt        <  1:3102761/67‑2 (MQ=255)

                                                            cTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt        <  1:204256/67‑2 (MQ=255)

                                                            cTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt        <  1:1633996/67‑2 (MQ=255)

                                                            cTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt        <  1:2906187/67‑2 (MQ=255)

                                                            cTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt        <  1:1970320/67‑2 (MQ=255)

                                                            cTTAACCGGCAGTAATTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCtgtgt        <  1:2551474/67‑2 (MQ=255)

                                                                 cTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTc  <  1:2661793/68‑1 (MQ=255)

CCTGCACTCATGGGTTCCAGGCATTCCCATCTGGTTATTTTCCCTCGTCATTACCCTCGCCTTAACTGGCAGTAACTTATTAAGCGTTAAAAACTACGGCGAATTTGAGTTCTGGCTGGCGCTGTGCAAAGTC  >  minE/1793482‑1793614

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