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	1,182,974	G→A	44.0%	G209G (GGC→GGT)	mipA ←	scaffolding protein for murein synthesizing machinery

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,182,974	0	G	A	44.0%	14.1 / 43.0	59	G209G (GGC→GGT)	mipA	scaffolding protein for murein synthesizing machinery
Reads supporting (aligned to +/- strand): ref base G (25/8); new base A (17/9); total (42/17)
Fisher's exact test for biased strand distribution p-value = 4.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCGGGCTGTCAGTAACTTCATCAGACAGACGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGCTGTCGTTCGGGTTATAGC  >  minE/1182909‑1183038

aTCGGGCTGTCAGTAACTTCATCAGACAGACGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCg                                                               >  1:104366/1‑69 (MQ=255)

aTCGGGCTGTCAGTAACTTCATCAGACAGACGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCg                                                               >  1:279155/1‑69 (MQ=255)

               aCTTCATCAGACAGACGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCt                                                 >  1:669579/1‑68 (MQ=255)

               aCTTCATCAGACAGACGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTg                                                >  1:447427/1‑69 (MQ=255)

               aCTTCATCAGACAGACGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTg                                                >  1:3264806/1‑69 (MQ=255)

               aCTTCATCAGACAGACGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTg                                                >  1:3115814/1‑69 (MQ=255)

               aCTTCATCAGACAGACGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTg                                                >  1:1316745/1‑69 (MQ=255)

               aCTTCATCAGACAGACGGGTGTAGCGTGCGGTACCGTAAACACTCAAGTCGCCGAGGAAGTTGTAGCTg                                                >  1:2010595/1‑69 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAg                                                         >  1:3324622/1‑56 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:3095314/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:860211/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:1271906/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:543487/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:2688537/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:2247874/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:322780/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:1115731/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:1821699/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:1821449/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:181820/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:1621398/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:1501490/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:1476180/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACCGTAAACACTCCAGTCACAGAGGAAGTTGTAGCTGgcg                                             >  1:1989129/1‑68 (MQ=255)

                   catcaGACAGACGGGTGTAGCGCGCGATACAGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGgcg                                             >  1:3047824/1‑68 (MQ=255)

                      cagacagaCGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCa                                         >  1:129237/1‑69 (MQ=255)

                      cagacagaCGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCa                                         >  1:638009/1‑69 (MQ=255)

                      cagacagaCGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCa                                         >  1:3360034/1‑69 (MQ=255)

                      cagacagaCGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCa                                         >  1:2844313/1‑69 (MQ=255)

                      cagacagaCGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCa                                         >  1:33833/1‑69 (MQ=255)

                                 gtgtAGTGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTaa                              <  1:1987286/69‑1 (MQ=255)

                                  tgtAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAg                             <  1:1356811/69‑1 (MQ=255)

                                  tgtAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAg                             <  1:3197695/69‑1 (MQ=255)

                                  tgtAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAg                             <  1:3208510/69‑1 (MQ=255)

                                  tgtAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAg                             <  1:3232300/69‑1 (MQ=255)

                                  tgtAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAg                             <  1:627958/69‑1 (MQ=255)

                                  tgtAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAg                             <  1:1885983/69‑1 (MQ=255)

                                  tgtAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAg                             <  1:1653402/69‑1 (MQ=255)

                                  tgtAGCGCGCGATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAg                             <  1:739508/69‑1 (MQ=255)

                                  tgtAGCGCGCAATACCGTAAACACTCCAGTCACCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAg                             <  1:715994/69‑1 (MQ=255)

                                           cGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGc                    >  1:2198925/1‑69 (MQ=255)

                                           cGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGc                    >  1:455610/1‑69 (MQ=255)

                                           cGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGc                    >  1:150517/1‑69 (MQ=255)

                                                  gTAAACACTCCAGTCGCCGAGGAAGTTGTATCTGGCGCTCAGCTCCAAGTAAGGGCTCCAGCTGTCGtt             >  1:1974442/1‑69 (MQ=255)

                                                  gTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAAGTAAGGGCTCGAGCTGTCGtt             >  1:334076/1‑69 (MQ=255)

                                                  gTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAAGTAAGGGCTCCAGCTGTCGtt             >  1:460414/1‑69 (MQ=255)

                                                  gTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAAGTAAGGGCTCCAGCTGTCGtt             >  1:1060185/1‑69 (MQ=255)

                                                  gTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAAGTAAGGGCTCCAGCTGTCGtt             >  1:2815454/1‑69 (MQ=255)

                                                  gTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAAGTAAGGGCTCCAGCTGTCGtt             >  1:2766466/1‑69 (MQ=255)

                                                  gTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAAGTAAGGGCTCCAGCTGTCGtt             >  1:2441470/1‑69 (MQ=255)

                                                  gTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAAGTAAGGGCTCCAGCTGTCGtt             >  1:2006834/1‑69 (MQ=255)

                                                  gTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAAGTAAGGGCTCCAGCTGTCGtt             >  1:1374125/1‑69 (MQ=255)

                                                       cacTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGCTGTCGTTCTGGt        <  1:2780730/69‑1 (MQ=255)

                                                       cacTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGCTGTCGTTCGGGt        <  1:446207/69‑1 (MQ=255)

                                                       cacTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGCTGTCGTTCGGGt        <  1:700408/69‑1 (MQ=255)

                                                       cacTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGCTGTCGTTCGGGt        <  1:1185253/69‑1 (MQ=255)

                                                              gTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGCTGTCTTTCGGGTTATAGc  <  1:3231579/68‑1 (MQ=255)

                                                              gTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGCTGTCGTTCGGGTTATAGc  <  1:445057/68‑1 (MQ=255)

                                                              gTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGCTGTCGTTCGGGTTATAGc  <  1:2589525/68‑1 (MQ=255)

ATCGGGCTGTCAGTAACTTCATCAGACAGACGGGTGTAGCGTGCGGTACCGTAAACACTCCAGTCGCCGAGGAAGTTGTAGCTGGCGCTCAGCTCCAGGTAAGGGCTCCAGCTGTCGTTCGGGTTATAGC  >  minE/1182909‑1183038

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