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
A1 F1 I1 R1	66	20.9	912876	97.7%	891879	114.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,969,883	A→T	N285Y (AAT→TAT)	wzzE →	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,969,883	0	A	T	94.7%	59.5 / ‑3.1	19	N285Y (AAT→TAT)	wzzE	Entobacterial Common Antigen (ECA) polysaccharide chain length modulation protein
Reads supporting (aligned to +/- strand): ref base A (0/1); new base T (11/7); total (11/8)
Fisher's exact test for biased strand distribution p-value = 4.21e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.11e-01

CGCAGTGCGACAGATGTACCTGCCGAGGAATTACCTGATTCAGAAATGTTCCTGCTTGGGCGTCCAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGAATCGGGCCATGTTAAACACCCTGAATGTTGGTCCAACCCTGGATCCGCGTTTTCAGACCTATCGCTATTTGCGTACGCCGGAAGAACCGGTAAAACGCGATAGCCCACGTCGTGCCTTCCTGATGATTATGTG  >  NC_000913/3969751‑3970016

cgcAGTGCGACAGATGTACCTGCCGAGGAATTACCTGATTCAGAAATGTTCCTGCTTGGGCGTCCAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCggg                                                                                                                                 <  1:406014/139‑1 (MQ=255)

        gACAGATGTACCTGCCGAGGAATTACCTGATTCAGAAATGTTCCTGCTTGGGCGTCCAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGAATCGGGCCATGTTa                                                                                                                         <  2:229424/139‑1 (MQ=255)

                 aCCTGCCGAGGAATTACCTGATTCAGAAATGTTCCTGCTTGGGCGTCCAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTg                                                                                                                >  2:88915/1‑139 (MQ=255)

                     gCCGAGGAATTACCTGATTCAGAAATGTTCCTGCTTGGGCGTCCAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTGAATg                                                                                                            >  2:356297/1‑139 (MQ=255)

                      ccGAGGAATTACCTGATTCAGAAATGTTCCTGCTTGGGCGTCCAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAac                                                                                                                      <  1:108436/128‑1 (MQ=255)

                      ccGAGGAATTACCTGATTCAGAAATGTTCCTGCTTGGGCGTCCAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAac                                                                                                                      >  2:108436/1‑128 (MQ=255)

                       cGAGGAATTACCTGATTCAGAAATGTTCCTGCTTGGGCGTCCAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTGAATGtt                                                                                                          >  1:143881/1‑139 (MQ=255)

                            aaTTACCTGATTCAGAAATGTTCCTGCTTGGGCGTCCAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTGAATGTTGGTcc                                                                                                     <  1:88915/139‑1 (MQ=255)

                                                          ggCGTCCAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTGAATGTTGGTCCAACCCTGGATCCGCGTTTTCAGACCTATCg                                                                       >  2:202976/1‑139 (MQ=255)

                                                           gCGTCCAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTGAATGTTGGTCCAACCCTGGATCCGCGTTTTCAGACCTATCGc                                                                      <  2:143881/139‑1 (MQ=255)

                                                                cAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTGAATGTTGGTCCAACCCTGGATCCGCGTTTTCAGACCTATCGCTAttt                                                                 >  2:330739/1‑139 (MQ=255)

                                                                        cAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTGAATGTTGGTCCAACCCTGGATCCGCGTTTTCAGACCTATCGCTATTTGCGTACGc                                                         >  1:401936/1‑139 (MQ=255)

                                                                        cAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTCAATGTTGGTCCAACCCTGGATCCGCGTCTTCAGACCTATCGCTATTTGCGTACGc                                                         >  2:18462/1‑139 (MQ=255)

                                                                         aGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTGAATGTTGGTCCAACCCTGGATCCGCGTTTTCAGACCTATCGCTATTTGCGTACGcc                                                        >  2:416001/1‑139 (MQ=255)

                                                                              cGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTGAATGTTGGTCCAACCCTGGATCCGCGTTTTCAGACCTATCGCTATTTGCGTACGCCGgaag                                                   <  1:330739/139‑1 (MQ=255)

                                                                                                                 tGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTGAATGTTGGTCCAACCCTGGATCCGCGTTTTCAGACCTATCGCTATTTGCGTACGCCGGAAGAACCGGTAAAAcgcg                                    <  1:416505/119‑1 (MQ=255)

                                                                                                                 tGATCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTGAATGTTGGTCCAACCCTGGATCCGCGTTTTCAGACCTATCGCTATTTGCGTACGCCGGAAGAACCGGTAAAAcgcg                                    >  2:416505/1‑119 (MQ=255)

                                                                                                                   aTCTCGACTATGATCAGTATCGGGCCATGTTAAACACCCTGAATGTTGGTCCAACCCTGGATCCGCGTTTTCAGACCTATCGCTATTTGCGTACGCCGGAAGAACCGGTAAAACGCGATAGCCCACGTCGTGCCTTCCt              <  1:202976/139‑1 (MQ=255)

                                                                                                                               aTCAGTATCGGGCCATGTTAAACACCCTGAATGTTGGTCCAACCCTGGATCCGCGTTTTCAGACCTATCGCTATTTGCGTACGCCGGAAGAACCGGTAAAACGCGATAGCCCACGTCGTGCCTTCCTGATGATTAtgtg  >  2:137284/1‑139 (MQ=255)

CGCAGTGCGACAGATGTACCTGCCGAGGAATTACCTGATTCAGAAATGTTCCTGCTTGGGCGTCCAATGCTTCAGGCTCGACTGGAAAATTTACAGGCCGTCGGTCCGGCCTTTGATCTCGACTATGATCAGAATCGGGCCATGTTAAACACCCTGAATGTTGGTCCAACCCTGGATCCGCGTTTTCAGACCTATCGCTATTTGCGTACGCCGGAAGAACCGGTAAAACGCGATAGCCCACGTCGTGCCTTCCTGATGATTATGTG  >  NC_000913/3969751‑3970016

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A