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	265,993	C→T	31.6%	E204E (GAG→GAA)	yajO ←	predicted oxidoreductase, NAD(P)‑binding

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	265,993	0	C	T	31.6%	33.4 / 16.9	41	E204E (GAG→GAA)	yajO	predicted oxidoreductase, NAD(P)‑binding
Reads supporting (aligned to +/- strand): ref base C (7/21); new base T (4/9); total (11/30)
Fisher's exact test for biased strand distribution p-value = 7.19e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACGGACGCGTCAGACGGCCCCTTGCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGATCCTGCA  >  minE/265937‑266060

caaggACGCGTCAGACGGCCCCGCGCCAGCGGTCTCCATGGAATCACCGCCACGCCTTCCTGATaa                                                            <  1:757872/63‑1 (MQ=255)

caaggACGCGTCAGACGGCCCCGCGCCAGCGGGCTCCATGGAATCACCGCCACGCCTTCCTGATaa                                                            <  1:1153374/63‑1 (MQ=255)

caaggACGCGTCAGACGGCCCCGCGCCAGCGGGCTCCATGGAATCACCGCCACGCCTTCCTGATaa                                                            <  1:2791567/63‑1 (MQ=255)

caaggACGCGTCAGACGGCCCCGCGCCAGCGGGCTCCATGGAATCACCGCCACGCCTTCCTGATaa                                                            <  1:2542732/63‑1 (MQ=255)

caaggACGCGTCAGACGGCCCCGCGCCAGCGGGCTCCATGGAATCACCGCCACGCCTTCCTGATaa                                                            <  1:2115977/63‑1 (MQ=255)

caaggACGCGTCAGACGGCCCCGCGCCAGCGGGCTCCATGGAATCACCGCCACGCCTTCCTGATaa                                                            <  1:2048167/63‑1 (MQ=255)

caaggACGCGTCAGACGGCCCCGCGCCAGCGGGCTCCATGGAATCACCGCCACGCCTTCCTGATaa                                                            <  1:1694372/63‑1 (MQ=255)

cACGGACGCGTCAGACGGCCCCTTGCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAacac                                                         <  1:1103315/69‑1 (MQ=255)

cACGGACGCGTCAGACGGCCCCTTGCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAacac                                                         <  1:409120/69‑1 (MQ=255)

cACGGACGCGTCAGACGGCCCCTTGCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAacac                                                         <  1:2378887/69‑1 (MQ=255)

cACGGACGCGTCAGACGGCCCCTTGCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAacac                                                         <  1:2001016/69‑1 (MQ=255)

cACGGACGCGTCAGACGGCCCCTTGCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAacac                                                         <  1:1588135/69‑1 (MQ=255)

cACGGACGCGTCAGACGGCCCCTTGCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAacac                                                         <  1:1099126/69‑1 (MQ=255)

cACGGACGCGTCAGACGGCCCCTTGCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAacac                                                         <  1:1192318/69‑1 (MQ=255)

  aggACGCGTCAGACGGCCCCGCGCCAGCGGGCTCCATGGAATCACCGCCACGCCTTCCTGATaa                                                            <  1:980858/63‑1 (MQ=255)

                       cgCCAGCGGGCTCCATGGAATCACCGCCACGCCTTCCTGATaa                                                            <  1:2769459/42‑1 (MQ=37)

                        gCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCtcttc                                  >  1:687475/1‑68 (MQ=255)

                        gCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCtcttc                                  >  1:2060850/1‑68 (MQ=255)

                        gCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCtcttc                                  >  1:2298865/1‑68 (MQ=255)

                        gCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCtcttc                                  >  1:2707222/1‑68 (MQ=255)

                              gggCTCCATGGAATCACCGCCACGCCTTCCTGATAACACAGCGGCAGCATCTCGCGCTCTTCTTCAc                             >  1:3422031/1‑67 (MQ=255)

                              gggCTCCATGGAATCACCGCCACGCCTTCCTGATAACACAGCGGCAGCATCTCGCGCTCTTCTTCACg                            >  1:828419/1‑68 (MQ=255)

                              gggCTCCATGGAATCACCGCCACGCCTTCCTGATAACACAGCGGCAGCATCTCGCGCTCTTCTTCACg                            >  1:2726780/1‑68 (MQ=255)

                              gggCTCCATGGAATCACCGCCACGCCTTCCTGATAACACAGCGGCAGCATCTCGCGCTCTTCTTCACg                            >  1:233112/1‑68 (MQ=255)

                                gCTCCATGGAATTACCGCCACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATa                         <  1:98858/69‑1 (MQ=255)

                                gCTCCATGGAATTACCGCCACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATa                         <  1:1297044/69‑1 (MQ=255)

                                           ttACCGCCACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGt              <  1:2341921/69‑1 (MQ=255)

                                             aCCGCCACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTa             >  1:1572527/1‑68 (MQ=255)

                                             aCCGCCACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTa             >  1:344559/1‑68 (MQ=255)

                                             aCCGCCACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTa             >  1:3329430/1‑68 (MQ=255)

                                                 ccACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTTGTGAt        <  1:1634480/69‑1 (MQ=255)

                                                 ccACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGAt        <  1:2503772/69‑1 (MQ=255)

                                                 ccACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGAt        <  1:914128/69‑1 (MQ=255)

                                                 ccACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGAt        <  1:1508873/69‑1 (MQ=255)

                                                 ccACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGAt        <  1:505637/69‑1 (MQ=255)

                                                 ccACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGAt        <  1:1399006/69‑1 (MQ=255)

                                                 ccACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGAt        <  1:3015885/69‑1 (MQ=255)

                                                 ccACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGAt        <  1:2772376/69‑1 (MQ=255)

                                                 ccACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGAt        <  1:2666493/69‑1 (MQ=255)

                                                 ccACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGAt        <  1:2543080/69‑1 (MQ=255)

                                                 ccACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGAt        <  1:1256745/69‑1 (MQ=255)

                                                       cctcctGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGATCCTGCa  <  1:3046768/69‑1 (MQ=255)

                                                       cctcctGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGATCCTGCa  <  1:1308351/69‑1 (MQ=255)

                                                       cctcctGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGATCCTGCa  <  1:1167385/69‑1 (MQ=255)

                                                       cctcctGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGATCCTGCa  <  1:1297253/69‑1 (MQ=255)

                                                       cctcctGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGATCCTGCa  <  1:594289/69‑1 (MQ=255)

                                                       cctcctGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGATCCTGCa  <  1:1965067/69‑1 (MQ=255)

                                                       cctcctGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGATCCTGCa  <  1:2183928/69‑1 (MQ=255)

                                                       cctcctGATAACACAGTGCTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGATCCTGCa  <  1:3075212/69‑1 (MQ=255)

                                                        ctcctGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGATCCTGCa  <  1:1692710/68‑1 (MQ=255)

CACGGACGCGTCAGACGGCCCCTTGCCAGCGGGCTCCATGGAATTACCGCCACGCCCTCCTGATAACACAGTGGTAGCATCTCGCGCTCTTCTTCACGATAAATCAGATTGTAGTGATCCTGCA  >  minE/265937‑266060

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