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
A3 F60 I1 R1	14	18.2	455004	92.7%	421788	134.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,279,705	G→A	A943V (GCA→GTA)	ebh_3 ←	Extracellular matrix‑binding protein ebh

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,279,705	0	G	A	93.3%	31.8 / ‑6.0	15	A943V (GCA→GTA)	ebh_3	Extracellular matrix‑binding protein ebh
Reads supporting (aligned to +/- strand): ref base G (0/0); major base A (4/10); minor base T (1/0); total (5/10)
Fisher's exact test for biased strand distribution p-value = 3.33e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCAT  >  USA300TCH1516_ALE/2279585‑2279822

gATTTTACTTCTGGTTTATTAGTTACATCTTTATTCATTGTCTGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCTCCt                                                                                                         <  2:72338/135‑1 (MQ=255)

 aTTCTACTTCTGGTTTACTTGTTACATCGTGATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGTTTGTGTTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTg                                                                                                        <  1:204614/135‑1 (MQ=255)

        ttCTGGTTTACGAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGc                                                                                                 <  2:91997/135‑1 (MQ=255)

         tCTGTTTTACTCGTTACATCGTTATCCATTATCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTGACCTGTTGCCGCa                                                                                                <  2:47551/135‑1 (MQ=255)

           tGGTTTACTAGATACATCGTTATACATTGTCGAACTGTTTGTTGATGCATCTAAAGTAGAATTGTTATGAGCCTGCGGTTTACAATTAGCATCATCAGTAGCTGATGTTATTGTGGTTTAACATGTTGTCGCATc                                                                                              >  2:181041/1‑135 (MQ=255)

                    ggTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATGGTTATTAGCTTACGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTAGCCGCATCACTattatt                                                                                     <  1:200749/134‑1 (MQ=255)

                      ttACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCAAATATTGACGCATAACTCTTATTTg                                                                                   >  2:52872/1‑135 (MQ=255)

                                          ggACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTTCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCt                                                               >  1:200635/1‑135 (MQ=255)

                                                            ttgacacTAGAATTGTTATTAGCTTGCGGTTTATCAGTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCTGAGAAGCGTCTGCTTTGCCATTAGCTgtc                                             <  2:212723/132‑1 (MQ=255)

                                                                          gTTATTAGCTTGCGGTTTATCATTTGCATCATCAATTGCTAAAATTAAAATAGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGtt                               >  1:29009/1‑135 (MQ=255)

                                                                                       tgTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTTTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTa                  <  1:215626/134‑1 (MQ=255)

                                                                                        gTTTATCATTTGCATCATCAGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTTCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTAt                 <  1:166599/135‑1 (MQ=255)

                                                                                          ttATCATTTGCATCATCAGTTGTTCTCATTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGATAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTAttt               <  1:37591/135‑1 (MQ=255)

                                                                                              gatgtGCATTATCAGTTGCTGATGTTACTGTTGTTTCACTTGTTGCCGCATCACTATTATTTGGTGTTGTCGGATAAGCGTTTCCTTTACTATTATCTTTTGTTTTAGATATGTTTGGTTGTCCAGTATTTTcgg           <  1:112213/131‑3 (MQ=255)

                                                                                                       catcaGTTGCTGATGTTACTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCAt  >  2:154841/1‑135 (MQ=255)

GATTCTACTTCTGGTTTACTAGTTACATCGTTATCCATTGTCGGACTGTTTGTTGATGCATCTACACTAGAATTGTTATTAGCTTGCGGTTTATCATTTGCATCATCAGTTGCTGATGTTGCTGTTGTTTCACCTGTTGCCGCATCACTATTATTTGGTGTTGTCGGAGAAGCGTCTGCTTTGCCATTAGCTGTCGTCTCAGATACGTTAGGTTGTCCAGTATTTTCTGGTGTTGCAT  >  USA300TCH1516_ALE/2279585‑2279822

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A