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	2,129,065	G→A	21.5%	A177A (GCG→GCA)	yhbW →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,129,065	0	G	A	21.5%	83.1 / 14.7	60	A177A (GCG→GCA)	yhbW	hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (19/28); new base A (3/10); total (22/38)
Fisher's exact test for biased strand distribution p-value = 3.38e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

GCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGATATGC  >  minE/2129019‑2129126

gCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTgg                                           <  1:2270691/67‑1 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTgg                                           <  1:2998850/67‑1 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTgg                                           <  1:3317239/67‑1 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTgg                                           <  1:3313194/67‑1 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTgg                                           <  1:1600575/67‑1 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGt                                          >  1:2661100/1‑68 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTc                                         >  1:1216656/1‑69 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTc                                         >  1:2923627/1‑69 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTc                                         >  1:802436/1‑69 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTc                                         >  1:3432725/1‑69 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTc                                         >  1:2688000/1‑69 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGCTc                                         >  1:1987689/1‑69 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTATTAGGCTCCAGCCTTTACAGTGCACAACTGGCGGCGCAGCTTGGTc                                         >  1:2214015/1‑69 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTATTAGGCTCCAGCCTTTACAGTGCACAACTGGCGGCGCAGCTTGGTc                                         >  1:693977/1‑69 (MQ=255)

gCGAGAAAATCCCCGTGTGGTTATTAGGCTCCAGCCTTTACAGTGCACAACTGGCGGCGCAGCTTGGTc                                         >  1:3202997/1‑69 (MQ=255)

           cccGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCa                                                             <  1:1501827/38‑1 (MQ=255)

           cccGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCa                                                             <  1:2888373/38‑1 (MQ=255)

           cccGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCa                                                             <  1:2559207/38‑1 (MQ=255)

           cccGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCa                                                             <  1:2923595/38‑1 (MQ=255)

           cccGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCa                                                             <  1:1292675/38‑1 (MQ=255)

           cccGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCa                                                             <  1:2451395/38‑1 (MQ=255)

           cccGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCa                                                             <  1:2104532/38‑1 (MQ=255)

                        tAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACt                 >  1:3305785/1‑69 (MQ=255)

                        tAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACt                 >  1:1003525/1‑69 (MQ=255)

                        tAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACt                 >  1:3408679/1‑69 (MQ=255)

                        tAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACt                 >  1:178136/1‑69 (MQ=255)

                        tAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACt                 >  1:700671/1‑69 (MQ=255)

                            cTCCAGCCTTTACAGTGCACAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTcgc             <  1:228963/69‑1 (MQ=255)

                            cTCCAGCCTTTACAGTGCACAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTcgc             <  1:2346190/69‑1 (MQ=255)

                            cTCCAGCCTTTACAGTGCACAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTcgc             <  1:3325790/69‑1 (MQ=255)

                            cTCCAGCCTTTACAGTGCACAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTcgc             <  1:2621858/69‑1 (MQ=255)

                            cTCCAGCCTTTACAGTGCACAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTcgc             <  1:2924847/69‑1 (MQ=255)

                            cTCCAGCCTTTACAGTGCACAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTcgc             <  1:128431/69‑1 (MQ=255)

                            cTCCAGCCTTTACAGTGCACAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTcgc             <  1:158505/69‑1 (MQ=255)

                             tCCAGCCTTTACAGTGCACAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTcgc             <  1:1141325/68‑1 (MQ=255)

                             tCCAGCCTTTACAGTGCACAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTcgc             <  1:2117685/68‑1 (MQ=255)

                                 gCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCg         <  1:486886/68‑1 (MQ=255)

                                 gCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCg         <  1:3272926/68‑1 (MQ=255)

                                 gCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCg         <  1:2864525/68‑1 (MQ=255)

                                 gCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCg         <  1:1679754/68‑1 (MQ=255)

                                 gCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCg         <  1:451341/68‑1 (MQ=255)

                                 gCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCg         <  1:2561190/68‑1 (MQ=255)

                                 gCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCg         <  1:3394232/68‑1 (MQ=255)

                                  ccTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGa       <  1:1333951/69‑1 (MQ=255)

                                    tttACAGCGCGCAACTGGCGGCGGAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCg         <  1:1131341/65‑1 (MQ=255)

                                     ttACAGTGCACAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTcgc             <  1:2091941/60‑1 (MQ=255)

                                     ttACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTGACACTTCGCGCCGGatat    <  1:511473/69‑1 (MQ=255)

                                     ttACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGatat    <  1:1758485/69‑1 (MQ=255)

                                     ttACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGatat    <  1:1709037/69‑1 (MQ=255)

                                      tACAGCGGGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGATATg   >  1:1689881/1‑69 (MQ=255)

                                      tACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGatat    >  1:247609/1‑68 (MQ=255)

                                      tACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGATATg   >  1:2840902/1‑69 (MQ=255)

                                      tACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGATATg   >  1:2806330/1‑69 (MQ=255)

                                      tACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGATATg   >  1:2469458/1‑69 (MQ=255)

                                      tACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGATATg   >  1:1356542/1‑69 (MQ=255)

                                      tACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGATATg   >  1:93227/1‑69 (MQ=255)

                                        cAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGATATGc  <  1:3082208/68‑1 (MQ=255)

                                        cAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGATATGc  <  1:1534431/68‑1 (MQ=255)

                                        cAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGATATGc  <  1:1396577/68‑1 (MQ=255)

                                         aGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGATATGc  <  1:2086175/67‑1 (MQ=255)

GCGAGAAAATCCCCGTGTGGTTGTTAGGCTCCAGCCTTTACAGCGCGCAACTGGCGGCGCAGCTTGGTCTGCCGTTTGCGTTTGCCTCACACTTCGCGCCGGATATGC  >  minE/2129019‑2129126

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