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	1,025,024	C→G	46.7%	A236A (GCG→GCC)	hdhA ←	7alpha‑hydroxysteroid dehydrogenase, NAD‑dependent

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,025,024	0	C	G	46.7%	4.6 / 58.7	53	A236A (GCG→GCC)	hdhA	7alpha‑hydroxysteroid dehydrogenase, NAD‑dependent
Reads supporting (aligned to +/- strand): ref base C (9/19); new base G (15/9); total (24/29)
Fisher's exact test for biased strand distribution p-value = 5.00e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

AGTGTATTAATTGAGCTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAATATCTTGCGGTTGGCCCAGAC  >  minE/1024958‑1025082

aGTGTATTAATTGAGCTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCgc                                                          <  1:784974/69‑1 (MQ=255)

      ttAATTGAGTTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTTGctgcag                                                     <  1:1581116/68‑1 (MQ=255)

      ttAATTGAGTTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGctgcag                                                     <  1:2650785/68‑1 (MQ=255)

      ttAATTGAGTTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGctgcag                                                     <  1:3302101/68‑1 (MQ=255)

      ttAATTGAGTTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGctgcag                                                     <  1:2863363/68‑1 (MQ=255)

      ttAATTGAGTTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGctgcag                                                     <  1:2565847/68‑1 (MQ=255)

      ttAATTGAGTTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGctgcag                                                     <  1:260601/68‑1 (MQ=255)

      ttAATTGAGTTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGctgcag                                                     <  1:15208/68‑1 (MQ=255)

      ttAATTGAGTTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGctgcag                                                     <  1:1075510/68‑1 (MQ=255)

      ttAATTGAGTTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGctgcag                                                     <  1:876302/68‑1 (MQ=255)

       tAATTGAGTTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGctgcag                                                     <  1:1202243/67‑1 (MQ=255)

       tAATTGAGCTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCgc                                                          <  1:822168/62‑1 (MQ=255)

       tAATTGAGCTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCgc                                                          <  1:2819699/62‑1 (MQ=255)

       tAATTGAGCTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCgc                                                          <  1:2261124/62‑1 (MQ=255)

                tCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAgg                                          <  1:218867/69‑1 (MQ=255)

                tCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAgg                                          <  1:2335592/69‑1 (MQ=255)

                 ccTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAgg                                          >  1:2689948/1‑68 (MQ=255)

                 ccTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAgg                                          >  1:1103597/1‑68 (MQ=255)

                 ccTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAgg                                          >  1:90948/1‑68 (MQ=255)

                 ccTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAgg                                          >  1:3060182/1‑68 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:386818/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:3248400/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:3400042/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:2627573/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:499798/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:693183/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:861436/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:985318/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:101268/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:1034961/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:1050116/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:1118688/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:1937497/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:2289885/1‑61 (MQ=255)

                   tGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTGGCTGCAGGCGAGc                                               >  1:2009897/1‑61 (MQ=255)

                              accGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCgcagca                                                      >  1:1027652/1‑43 (MQ=255)

                              accGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCa                                              >  1:2871288/1‑51 (MQ=255)

                                    gaCGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAat                      <  1:3036313/69‑1 (MQ=255)

                                    gaCGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAat                      <  1:2648893/69‑1 (MQ=255)

                                    gaCGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAat                      <  1:2443755/69‑1 (MQ=255)

                                    gaCGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAat                      <  1:2339461/69‑1 (MQ=255)

                                    gaCGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAat                      <  1:1404128/69‑1 (MQ=255)

                                    gaCGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAat                      <  1:3245010/69‑1 (MQ=255)

                                    gaCGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAat                      <  1:1954363/69‑1 (MQ=255)

                                    gaCGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAat                      <  1:1975976/69‑1 (MQ=255)

                                    gaCGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAat                      <  1:3093634/69‑1 (MQ=255)

                                                 tGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAgg                                          >  1:624216/1‑36 (MQ=255)

                                                 tGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAgg                                          >  1:815174/1‑36 (MQ=255)

                                                 tGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAgg                                          >  1:2264893/1‑36 (MQ=255)

                                                        tttcccAGCGCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAATATCTTGCGGTTGGCCCAGAc  <  1:419344/66‑1 (MQ=255)

                                                        ttACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAATATCTTGCGGTTGGCCCAGAc  <  1:1993248/69‑1 (MQ=255)

                                                        ttACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAATATCTTGCGGTTGGCCCAGAc  <  1:939049/69‑1 (MQ=255)

                                                        ttACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAATATCTTCCGGTTGGCCCAGAc  <  1:127514/69‑1 (MQ=255)

AGTGTATTAATTGAGCTCCTGTACCCCACCACCGGAGACGGTGAGAATTTGTCCGCTTACCCAGCTCGCAGCAGGCGAGCAAAGGAACAGCGCTGCGTTAGCAATATCTTGCGGTTGGCCCAGAC  >  minE/1024958‑1025082

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