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	2,845,845	T→C	33.8%	Y115Y (TAT→TAC)	yjeM →	predicted transporter

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,845,845	0	T	C	33.8%	44.1 / 32.7	62	Y115Y (TAT→TAC)	yjeM	predicted transporter
Reads supporting (aligned to +/- strand): ref base T (25/16); new base C (5/16); total (30/32)
Fisher's exact test for biased strand distribution p-value = 7.46e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01

TCTTATATCATCTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGTGGTTGGTCTGCT  >  minE/2845780‑2845910

tctTATATCATCTGGATGGTGAGTACCTCCGCGAAAG‑TTGGGTACCGTTCTCAACATTCCTCTATGGt                                                                <  1:207588/68‑1 (MQ=255)

 ctTATATCATCTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGt                                                                <  1:2611698/68‑1 (MQ=255)

 ctTATATCATCTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGt                                                                <  1:1875518/68‑1 (MQ=255)

 ctTATATCATCTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGt                                                                <  1:651282/68‑1 (MQ=255)

 ctTATATCATCTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGt                                                                <  1:3281662/68‑1 (MQ=255)

 ctTATATCATCTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGt                                                                <  1:1585671/68‑1 (MQ=255)

 ctTATATCATCTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGt                                                                <  1:1327036/68‑1 (MQ=255)

 ctTATATCATCTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGt                                                                <  1:1575406/68‑1 (MQ=255)

 ctTATATCATCTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGt                                                                <  1:780240/68‑1 (MQ=255)

         atcTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATg                                                       >  1:2243728/1‑69 (MQ=255)

         atcTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATg                                                       >  1:1339895/1‑69 (MQ=255)

         atcTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATg                                                       >  1:1406217/1‑69 (MQ=255)

                          cTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCg                                                            >  1:1878035/1‑47 (MQ=255)

                          cTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAt                                      >  1:2978694/1‑69 (MQ=255)

                          cTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAt                                      >  1:1337565/1‑69 (MQ=255)

                          cTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAt                                      >  1:2977106/1‑69 (MQ=255)

                          cTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAt                                      >  1:197774/1‑69 (MQ=255)

                          cTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAt                                      >  1:2179564/1‑69 (MQ=255)

                          cTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAt                                      >  1:753063/1‑69 (MQ=255)

                           tCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAtt                                     >  1:611088/1‑69 (MQ=255)

                           tCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAtt                                     >  1:3056100/1‑69 (MQ=255)

                           tCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAtt                                     >  1:3224203/1‑69 (MQ=255)

                           tCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAtt                                     >  1:841482/1‑69 (MQ=255)

                           tCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAtt                                     >  1:945400/1‑69 (MQ=255)

                           tCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAtt                                     >  1:1156990/1‑69 (MQ=255)

                           tCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAtt                                     >  1:959716/1‑69 (MQ=255)

                           tCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTAt                                      >  1:3200898/1‑68 (MQ=255)

                            ccGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTg                                    >  1:3188613/1‑69 (MQ=255)

                            ccGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTg                                    >  1:1092812/1‑69 (MQ=255)

                            ccGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTg                                    >  1:2676380/1‑69 (MQ=255)

                            ccGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTg                                    >  1:2662136/1‑69 (MQ=255)

                            ccGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTg                                    >  1:2366409/1‑69 (MQ=255)

                             cgcgAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGt                                                                <  1:1860627/40‑1 (MQ=255)

                                           tACCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACT‑GCATATTGCCGGACTGGAGCCTAc                    <  1:1585976/69‑1 (MQ=255)

                                            aCCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTAc                    <  1:755544/69‑1 (MQ=255)

                                            aCCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTAc                    <  1:499300/69‑1 (MQ=255)

                                            aCCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTAc                    <  1:1527320/69‑1 (MQ=255)

                                            aCCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTAc                    <  1:31009/69‑1 (MQ=255)

                                            aCCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTAc                    <  1:1967745/69‑1 (MQ=255)

                                            aCCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTAc                    <  1:763808/69‑1 (MQ=255)

                                            aCCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTAc                    <  1:2094125/69‑1 (MQ=255)

                                            aCCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTAc                    <  1:2932393/69‑1 (MQ=255)

                                            aCCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTAc                    <  1:274391/69‑1 (MQ=255)

                                            aCCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTAc                    <  1:2731393/69‑1 (MQ=255)

                                            aCCGTTCTCAACATTCCTCTACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTAc                    <  1:26926/69‑1 (MQ=255)

                                               gTTCTCAACATTCCTCTACGGTAGCGACATGTCCCAGCACTGGCATATTGCCGGACTGGAGCCTAc                    <  1:719417/66‑1 (MQ=255)

                                                       cATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttg         <  1:2985877/69‑1 (MQ=255)

                                                       cATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttg         <  1:1379444/69‑1 (MQ=255)

                                                        aTTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttgg        <  1:1188770/69‑1 (MQ=255)

                                                         ttCCTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttggt       >  1:1134005/1‑69 (MQ=255)

                                                         ttCCTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttggt       >  1:539756/1‑69 (MQ=255)

                                                         ttCCTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttggt       >  1:2818107/1‑69 (MQ=255)

                                                         ttCCTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttggt       >  1:2090173/1‑69 (MQ=255)

                                                         ttCCTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttggt       >  1:145979/1‑69 (MQ=255)

                                                         ttCCTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttggt       >  1:1244319/1‑69 (MQ=255)

                                                         ttCCTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttggt       >  1:1171275/1‑69 (MQ=255)

                                                           ccTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttg         <  1:472175/65‑1 (MQ=255)

                                                           ccTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttg         <  1:2686242/65‑1 (MQ=255)

                                                           ccTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGtggttg         <  1:115046/65‑1 (MQ=255)

                                                              ctACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTACGCAGGTGGTTGGTctgct  <  1:603570/69‑1 (MQ=255)

                                                              ctACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTACGCAGGTGGTTGGTctgct  <  1:3134408/69‑1 (MQ=255)

                                                              ctACGGTAGCGACATGACCCAGCACTGGCATATTGCCGGACTGGAGCCTACGCAGGTGGTTGGTctgct  <  1:2994119/69‑1 (MQ=255)

TCTTATATCATCTGGATGGTGAGTACCTCCGCGAAAGTTTGGGTACCGTTCTCAACATTCCTCTATGGTAGCGACATGACCCAGCACTGGCGTATTGCCGGACTGGAGCCTACGCAGGTGGTTGGTCTGCT  >  minE/2845780‑2845910

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