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 F18 I1 R1	9	30.2	693202	94.8%	657155	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,513,930	A→T	L413F (TTA→TTT)	USA300HOU_RS07375 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,513,930	0	A	T	100.0%	128.7 / NA	40	L413F (TTA→TTT)	USA300HOU_RS07375	hypothetical protein
Reads supporting (aligned to +/- strand): ref base A (0/0); new base T (13/27); total (13/27)

TGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTT  >  USA300TCH1516_ALE/1513801‑1514062

tgtatgtaTCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAgg                                                                                                                           <  1:141370/141‑1 (MQ=255)

  tatgtatCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGat                                                                                                                         <  2:29611/141‑1 (MQ=255)

  gatgtatCGCATTTTTAGTATGTATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGat                                                                                                                         <  2:83871/140‑1 (MQ=255)

        tCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTaa                                                                                                                   <  1:49092/141‑1 (MQ=255)

          gcgttattaGTAGCCATTGGCATGGGGTTTGTCTATTGGATAAAGCATACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATg                                                                                                                 <  2:68972/138‑1 (MQ=255)

          aatttATTAGTAGCCATTAGCATGGGGTTTGTCACTTGGATAAAGCGGACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATg                                                                                                                 <  2:280380/139‑1 (MQ=255)

            tttATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGCAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGcc                                                                                                               <  2:307961/141‑1 (MQ=255)

               attaGTAGCCATTGGCATGGGGTTTGAATCTTGGATAAAGCGTACAAAAAATAATGCAATAAAAGTACCACATCGCGTAAAAAAAACAGCATCTATATCACTAATAATATGATTTATTGTATTAGTATTATTAATCCCata                                                                                                            >  2:117484/1‑140 (MQ=255)

                    aagCAATAGGCATGGGGTTTGTATCTTGGATAAAGCGTAAAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTg                                                                                                       <  2:253045/140‑1 (MQ=255)

                       ccATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACAACGCGTAAAAAACCCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATTCCATTATTTTGAt                                                                                                    >  2:260549/1‑141 (MQ=255)

                           tgggagggggTTTGTCTCTTGGATAAAGCGTAGAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATc                                                                                                <  2:89799/135‑1 (MQ=255)

                           tGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATc                                                                                                >  2:215762/1‑141 (MQ=255)

                             gCATGGGGTTTGTCTCCTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCAc                                                                                              <  1:61949/141‑1 (MQ=255)

                                 ggggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTAt                                                                                          >  2:344511/1‑141 (MQ=255)

                                 ggggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTAt                                                                                          >  2:67388/1‑141 (MQ=255)

                                   ggTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATcc                                                                                        <  1:334063/141‑1 (MQ=255)

                                            ctTGGATAAAGCGTACCTGAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTta                                                                               <  1:129738/141‑1 (MQ=255)

                                             ttGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTtat                                                                              <  1:157063/141‑1 (MQ=255)

                                                aaTAAAGCGTACAAAAAATACTGAAATAAAAGTACCAAATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTtatact                                                                           <  2:341164/140‑3 (MQ=255)

                                                   aaaGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                        <  1:1445/141‑1 (MQ=255)

                                                   aaaGCATACAAAAAATACTGTAATAAAATAACCACATCGCGTAAAAAAAACAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATTCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGa                                                                        <  1:124267/141‑1 (MQ=255)

                                                      gCGTACAAAAAATACTGCACTAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                     <  1:192956/141‑1 (MQ=255)

                                                      gCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGT‑AAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTa                                                                    <  1:301636/141‑1 (MQ=255)

                                                      gCGTAAAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAAtt                                                                     <  1:23003/141‑1 (MQ=255)

                                                       agTAAAAAAAATACCGCAATAAAAGTAAAAAAAAAAAAAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTa                                                                    <  2:192922/140‑1 (MQ=255)

                                                               aaaTACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATtata                                                            >  1:205542/1‑141 (MQ=255)

                                                                      gCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTaaa                                                     <  1:194933/141‑1 (MQ=255)

                                                                                      aTCGCGTAAAAAAACTATCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAAc                                     <  2:61717/141‑1 (MQ=255)

                                                                                        ggcgTAAAAGAACCAGAATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACaa                                   <  2:105509/140‑1 (MQ=255)

                                                                                        agcgTAAAAAAAACAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAATATCGTCGTGCTAAACaa                                   <  2:231322/140‑1 (MQ=255)

                                                                                                    ccAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaa                       >  2:206916/1‑141 (MQ=255)

                                                                                                     cAGCATCTATATCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTaaa                      >  2:17951/1‑141 (MQ=255)

                                                                                                               atCACTCATAATATGTTTTATTGTATTAGGATTCTTGAAGCCATTATTTGGATTATCACTTATCCTTGTATTTATACTTGAATTAATATTCTATATTAAAGATCATAGTTCTAAAAAATAATGCACTTAAAGTTTTTAACt            >  2:192394/1‑141 (MQ=255)

                                                                                                               atCACTCATAATATGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGATTTAATATTATATATTAAAGATCTTCGTGCTAAACTATAATGCACTTAAAGTTTTGAACt            >  2:21971/1‑141 (MQ=255)

                                                                                                                       taataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGCACTGACGAAAt    >  2:162192/1‑141 (MQ=255)

                                                                                                                       taataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAt    >  1:69186/1‑141 (MQ=255)

                                                                                                                        aataTGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAtt   >  1:50644/1‑141 (MQ=255)

                                                                                                                         atatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAttt  <  1:335733/141‑1 (MQ=255)

                                                                                                                         atatGTTTTATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAttt  <  2:160183/141‑1 (MQ=255)

                                                                                                                         atatGTTTTATTGTATTAGGATTATTAATGCAATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTTCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAAttt  <  2:153268/141‑1 (MQ=255)

TGTATGTATCGCTTTATTAGTAGCCATTGGCATGGGGTTTGTCTCTTGGATAAAGCGTACAAAAAATACTGCAATAAAAGTACCACATCGCGTAAAAAAACCAGCATCTATATCACTCATAATATGTTTAATTGTATTAGGATTATTAATGCCATTATTTGGATTATCACTTATCCTTGTATTTATAATTGAATTAATATTATATATTAAAGATCGTCGTGCTAAACAATAATGCACTTAAAGTTTTGAACTGACGAAATTT  >  USA300TCH1516_ALE/1513801‑1514062

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A