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
A23 F74 I1 R1	13	20.1	450294	97.3%	438136	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	2,028,049	A→G	V199A (GTT→GCT)	USA300HOU_RS10230 ←	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	2,028,049	0	A	G	100.0%	96.2 / NA	27	V199A (GTT→GCT)	USA300HOU_RS10230	hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base G (16/11); total (16/11)

GCATTGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTA  >  USA300TCH1516_ALE/2027913‑2028183

gCATTGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCttt                                                                                                                                    >  2:162060/1‑141 (MQ=255)

gCATTGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCtgt                                                                                                                                    >  2:79739/1‑139 (MQ=255)

  aTTGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTtat                                                                                                                                  <  2:108670/141‑1 (MQ=255)

      aaCCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGa                                                                                                                              <  1:134788/141‑1 (MQ=255)

         cAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGAttt                                                                                                                           <  2:30138/141‑1 (MQ=255)

         cAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGAttt                                                                                                                           <  2:162794/141‑1 (MQ=255)

                           ggTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACt                                                                                                         >  2:128990/1‑141 (MQ=255)

                           ggTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACt                                                                                                         >  1:219281/1‑141 (MQ=255)

                                     tAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATaaaaa                                                                                               >  1:14092/1‑141 (MQ=255)

                                       aaTCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAagc                                                                                             >  1:176648/1‑141 (MQ=255)

                                         tCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAagcag                                                                                           >  1:65105/1‑141 (MQ=255)

                                            ccTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTa                                                                                        >  2:58758/1‑141 (MQ=255)

                                                    tctcCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTaaa                                                                                <  2:184150/141‑1 (MQ=255)

                                                               cGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTa                                                                     >  1:29286/1‑141 (MQ=255)

                                                               cGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTa                                                                     >  2:162517/1‑141 (MQ=255)

                                                                                 aaCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCCGCTTTATATGATTTTTCATTCACGTAATTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAAc                                                   <  2:179077/141‑1 (MQ=255)

                                                                                 aaCTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAAc                                                   <  1:111025/141‑1 (MQ=255)

                                                                                         aGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACtt                                           <  1:180980/141‑1 (MQ=255)

                                                                                               ccGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTa                                     <  2:65105/141‑1 (MQ=255)

                                                                                                                 cAATATGAATATTGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAAcaacaa                   >  1:26371/1‑141 (MQ=255)

                                                                                                                            ttGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTAttt        <  1:162517/141‑1 (MQ=255)

                                                                                                                            ttGTTATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTAttt        <  2:29286/141‑1 (MQ=255)

                                                                                                                                tATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCt    >  1:97447/1‑141 (MQ=255)

                                                                                                                                tATTTTCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCt    >  1:118923/1‑141 (MQ=255)

                                                                                                                                  ttttCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTa  >  1:102749/1‑141 (MQ=255)

                                                                                                                                  ttttCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTa  >  1:222367/1‑141 (MQ=255)

                                                                                                                                  gtttCAGCTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTa  >  1:213469/2‑141 (MQ=255)

GCATTGAACCAATTGTTCTAATGTAGTGGTTCATCGATAAATCACCTCTACGTCTCCGATAAACGTTGATACGTAGATATTAACTGTATAGTTATCCGGTTTCATCATTTCTTCAATATGAATATTGTTATTTTCAACTTTATATGATTTTTCATTCACGTAAGTACTTCCATAAAAAGCAGCTACATGTAAATTAATATTGTAATTAACCGGCAATATAACCTGCACTTTACCTAAAATGTGTCTAACAACAATGGTATTATTTTCCTTA  >  USA300TCH1516_ALE/2027913‑2028183

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A