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
A13 F1 I1 R1	86	24.1	1002126	98.1%	983085	121.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	585,217	C→T	W139* (TGG→TGA)	ompT ←	DLP12 prophage, outer membrane protease VII, outer membrane protein 3b

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	585,217	0	C	T	100.0%	92.2 / NA	27	W139* (TGG→TGA)	ompT	DLP12 prophage, outer membrane protease VII, outer membrane protein 3b
Reads supporting (aligned to +/- strand): ref base C (0/0); new base T (12/15); total (12/15)

GGGAAGGAGCCGATATCATCTCTGAATCCCTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGCCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCCAGTCCTGATCG  >  NC_000913/585083‑585328

gggAAGGAGCCGATATCATCTCTGAATCCCTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGagtcagc                                                                                                             <  2:50974/139‑1 (MQ=255)

 ggAAGGAGCCGATATCATCTCTGAATCCCTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGagtcagcc                                                                                                            >  1:493101/1‑139 (MQ=255)

                 atcTCTGAATCCCTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCa                                                                                            >  2:439860/1‑139 (MQ=255)

                           cccTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCTGATCAAATTCGTTgg                                                                                  <  1:377477/139‑1 (MQ=255)

                                       cTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGtt                                                                      <  1:336255/139‑1 (MQ=255)

                                               ataGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCa                                                              >  2:463532/1‑139 (MQ=255)

                                                taGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAg                                                             <  1:354658/139‑1 (MQ=255)

                                                 aGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAgg                                                            >  1:34029/1‑139 (MQ=255)

                                                    aaCCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGgtg                                                         >  2:164732/1‑139 (MQ=255)

                                                     accaccTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGgtgt                                                        <  2:486781/139‑1 (MQ=255)

                                                        accTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTa                                                     <  2:251367/139‑1 (MQ=255)

                                                          ctctGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGtt                                                                      <  1:369113/120‑1 (MQ=255)

                                                          ctctGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGtt                                                                      >  2:369113/1‑120 (MQ=255)

                                                          ctctGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACt                                                   >  2:169303/1‑139 (MQ=255)

                                                             tGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTgg                                                                                  >  1:245009/1‑105 (MQ=255)

                                                             tGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTgg                                                                                  <  2:245009/105‑1 (MQ=255)

                                                                   tAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGt                                          >  2:396997/1‑139 (MQ=255)

                                                                                    tCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTAc                         <  2:493101/139‑1 (MQ=255)

                                                                                     ccTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCgggg                             <  2:146591/134‑1 (MQ=255)

                                                                                     ccTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCgggg                             >  1:146591/1‑134 (MQ=255)

                                                                                              cGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAatccat               <  1:304625/139‑1 (MQ=255)

                                                                                                gCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAatccatcc             >  2:9958/1‑139 (MQ=255)

                                                                                                      aGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGtt                                                                      <  2:390303/76‑1 (MQ=255)

                                                                                                      aGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGtt                                                                      >  1:390303/1‑76 (MQ=255)

                                                                                                       gTCCCAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCCAGTCCTg      <  2:469157/139‑1 (MQ=255)

                                                                                                         cccAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCCAGTCCTGAt    <  2:20595/139‑1 (MQ=255)

                                                                                                           cAGGCGGTAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCCAGTCCTGATCg  <  1:164732/139‑1 (MQ=255)

                                                                                                                  tAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGGTCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAat                   <  1:358401/115‑1 (MQ=255)

                                                                                                                  tAATTGGGTTCGTTGAGGAGTCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAat                   >  2:358401/1‑115 (MQ=255)

GGGAAGGAGCCGATATCATCTCTGAATCCCTCCTCAGAACTGTAGATATAGGAACCACCTCTGGCTGTAAAGCTATAACGGCTTTCCTGATATCCGGCCATGAGTCCCAGGCGGTAATTGGGTTCGTTGAGGAGCCAGCCTTTGATATTCAGATCAAATTCGTTGGCATAATTGAGTTGTGTATCAGGGTGTCTACTTTCATCCGTCCAGGTTCCGGGGTTACTGGAATCCATCCAGTCCTGATCG  >  NC_000913/585083‑585328

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A