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
A25 F36 I0 R2	1302	104.9	4551290	96.3%	4382892	111.1

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	860,154	A→T	30.0%	intergenic (‑126/+20)	ybiV ← / ← ybiW	sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase/putative pyruvate formate lyase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	860,154	0	A	T	30.0%	27.8 / 14.8	20	intergenic (‑126/+20)	ybiV/ybiW	sugar phosphatase; fructose‑1‑P/ribose‑5‑P/glucose‑6‑P phosphatase/putative pyruvate formate lyase
Reads supporting (aligned to +/- strand): ref base A (7/7); new base T (3/3); total (10/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.42e-01

AATAACAATGTGACGCAGAGCACAAATTATATTTCGAATGAAAGTAAGGATGAAATTGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCGATGATATCGTCCTGAGCGTCTGGAGAGAGCGCGGTGAAGAACGCGGAATAGCCCGCGACACGCACTACCAGATCGCGATA  >  NC_000913/860068‑860278

aataaCAATGTGACGCAGAGCACAAATTATATTTCGAATGAAAGTAAGGATGAAATTGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCata                                                                                                 <  1:985141/116‑1 (MQ=255)

aataaCAATGTGACGCAGAGCACAAATTATATTTCGAATGAAAGTAAGGATGAAATTGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCata                                                                                                 >  2:985141/1‑116 (MQ=255)

             cGCAGAGCACAAATTATATTTCGAATGAAAGTAAGGATGAGATTGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCgaggag                                                                                                            <  4:672197/92‑1 (MQ=255)

             cGCAGAGCACAAATTATATTTCGAATGAAAGTAAGGATGAAATTGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCgaggag                                                                                                            >  3:672197/1‑92 (MQ=255)

                         aTTATATTTCGAATGAAAGTAAGGATGAAATTGATGATGTGAATGATTTAGCCCGGCGGCGTCGtcgccg                                                                                                                      <  4:583763/70‑1 (MQ=38)

                         aTTATATTTCGAATGAAAGTAAGGATGAAATTGATGATGTGAATGATTTAGCCCGGCGGCGTCGtcgccg                                                                                                                      >  3:583763/1‑70 (MQ=39)

                                    aaTGAAAGTAAGGATGAAATTGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCGATGATATCGt                                                                        <  1:563521/105‑1 (MQ=255)

                                    aaTGAAAGTAAGGATGAAATTGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCGATGATATCGt                                                                        >  2:563521/1‑105 (MQ=255)

                                                 aTGAAATTGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCATATGt                                                                                              >  3:508323/1‑70 (MQ=255)

                                                 aTGAAATTGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCATATGt                                                                                              <  4:508323/70‑1 (MQ=255)

                                                       ttGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCg                                                                                  <  3:132663/76‑1 (MQ=255)

                                                       ttGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCg                                                                                  >  4:132663/1‑76 (MQ=255)

                                                       ttGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCGATGGTATCGTCCTGAg                                                                  >  3:369560/1‑92 (MQ=255)

                                                       ttGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCGATGGTATCGTCCTGAg                                                                  <  4:369560/92‑1 (MQ=255)

                                                                     gATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCgatgat                                                                             >  3:516338/1‑67 (MQ=255)

                                                                     gATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCgatgat                                                                             <  4:516338/67‑1 (MQ=255)

                                                                               ggcggcGTCGTCGCCGGGCCGAGGAGATTACAGCATATGTTc                                                                                            <  2:528882/42‑1 (MQ=25)

                                                                               ggcggcGTCGTCGCCGGGCCGAGGAGATTACAGCATATGTTc                                                                                            >  1:528882/1‑42 (MQ=25)

                                                                               ggcggcGTCGTCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCGATGATATCGTCCTGAGCGTCTGGAGAGAGCGCGGTGAAGAACGCGGAATAGCCCGCGACACGCACTACCAGa          <  3:194859/124‑1 (MQ=255)

                                                                               ggcggcGTCGTCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCGATGATATCGTCCTGAGCGTCTGGAGAGAGCGCGGTGAAGAACGCGGAATAGCCCGCGACACGCACTACCAGa          >  4:194859/1‑124 (MQ=255)

                                                                                 cgacgaCGCCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCGATGATATCGTCCTGAGCGTCTGGAGAGAGCGCGGTGAAGAACGCGGAATAGCCCGCGACACGCACTACCAGATCGCGATa  >  3:1020296/1‑130 (MQ=255)

                                                                                 cgacgaCGCCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCGATGATATCGTCCTGAGCGTCTGGAGAGAGCGCGGTGAAGAACGCGGAATAGCCCGCGACACGCACTACCAGATCGCGATa  <  4:1020296/130‑1 (MQ=255)

AATAACAATGTGACGCAGAGCACAAATTATATTTCGAATGAAAGTAAGGATGAAATTGATGATGTGAATGATTTAGCCCGGCGACGACGCCGCCGGGCCGAGGAGATTACAGCATATGTTCAGTACGGGCGATGATATCGTCCTGAGCGTCTGGAGAGAGCGCGGTGAAGAACGCGGAATAGCCCGCGACACGCACTACCAGATCGCGATA  >  NC_000913/860068‑860278

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 30 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A