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
A19 F106 I1 R1	27	57.4	1363720	95.8%	1306443	135.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,605,275	G→T	R199L (CGT→CTT)	Int‑Tn_2 →	Transposase from transposon Tn916

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,605,275	0	G	T	97.1%	94.8 / NA	34	R199L (CGT→CTT)	Int‑Tn_2	Transposase from transposon Tn916
Reads supporting (aligned to +/- strand): ref base G (0/0); major base T (18/15); minor base A (1/0); total (19/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTACAATTATCCAAATGAATATTTGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACGTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAGA  >  USA300TCH1516_ALE/1605144‑1605404

ttACAATTATCCAAATGAATATTTGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGa                                                                                                                                >  2:493308/1‑135 (MQ=255)

                  atatTTGTTAACTAATGTCAAAATTCATAAAACAAAAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGataa                                                                                                              >  1:216309/1‑135 (MQ=255)

                  atatTTGTCAACTAATGTCAAAATTCCTAAAAGAAGAAACACAATCGAGGATATAGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGataa                                                                                                              >  2:83377/1‑135 (MQ=255)

                           aagtAATATCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTaca                                                                                                     <  1:261128/132‑1 (MQ=255)

                                     aaaaTTCCTAAAAGAAGAAAAACAATAAAGGATAACGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTAAACAAGCGAAAt                                                                                           >  1:25178/1‑135 (MQ=255)

                                       aaTTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCg                                                                                         >  2:332878/1‑135 (MQ=255)

                                                 agaagaAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAAtt                                                                               >  2:225599/1‑135 (MQ=255)

                                                 agaagaAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAAtt                                                                               >  2:578265/1‑135 (MQ=255)

                                                      aaaaaCAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAg                                                                          >  2:357342/1‑135 (MQ=255)

                                                         aaCAAAAGAGAATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCAt                                                                       <  2:600560/135‑1 (MQ=255)

                                                          aCAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATc                                                                      >  2:671887/1‑135 (MQ=255)

                                                                    atatCGAAAAAGATGAATCTAAAATGTACAACAAATAAAAAATGAACCAAGTACTCCAGATACATGATCATATACTCAAAGATAAAAAGTTACACAAACGAAATCGCATTTTAATTGCCAGCATCTTAGAAATaa                                                            >  1:265132/1‑134 (MQ=255)

                                                                             aaGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTaa                                                   <  2:40193/135‑1 (MQ=255)

                                                                                aTGACTCTAAAATTTAAAACTATTTAGAATTGAACTCAGTACTAAAGATAATTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTg                                                <  1:249513/135‑1 (MQ=255)

                                                                                aTGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCGTCTTAGAAGTACAGGCTTTAACTg                                                <  2:80053/135‑1 (MQ=255)

                                                                                 tGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTgg                                               >  2:269930/1‑135 (MQ=255)

                                                                                                        ttgAAATTAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAg                        <  1:606015/133‑1 (MQ=255)

                                                                                                            aaTGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTATAGGTTTTAACTGGTATGTGCATAGGAGAACTACAAGCACt                    <  1:115803/135‑1 (MQ=255)

                                                                                                            aaTGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACt                    <  1:493308/135‑1 (MQ=255)

                                                                                                            aaTGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACt                    <  1:671887/135‑1 (MQ=255)

                                                                                                            aaTGAACCAAGTCCTACAGATACTTCATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACt                    <  1:351761/135‑1 (MQ=255)

                                                                                                              tGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAATTGGTATGCGCATAGGAGAACTACAAGCACTGc                  <  1:40519/135‑1 (MQ=255)

                                                                                                              tGAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGc                  >  2:250454/1‑135 (MQ=255)

                                                                                                               gccccAAGTCCTACATATACTTAATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCa                 >  1:9738/4‑135 (MQ=255)

                                                                                                               gAACCAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAACGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTCCAGGCTTTACCTGGTATCCGCATAGGAGACCTCCAGGCACTGcg                 >  2:448156/1‑134 (MQ=255)

                                                                                                                   cAAGTCCTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTCCAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGaa             >  2:35085/1‑135 (MQ=255)

                                                                                                                         cTACAGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAAGCGCATTTTAATTGCCAGCATCTTAAAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGGACTGCAGGAAAAAGat       >  2:102336/1‑135 (MQ=255)

                                                                                                                            cAGATACTTGATCATGTACTAAATGATAATAAGTTACACGAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACCACAAGCACTGTAGGAAAAAGAtata    >  1:349413/1‑135 (MQ=255)

                                                                                                                             aGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCCTAGGAGCACCACAAGCACTGCAGGCAACAgcgatcg   >  2:372685/1‑129 (MQ=255)

                                                                                                                             aGATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAg   >  2:602754/1‑135 (MQ=255)

                                                                                                                              gATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCTCATTTTACTTGCCAGCATCTTAGAACTACAGGCTTTAACTGGTATGCGCATTGGAGAACTTCAAGCATTTCATGAAAAAGATATAgc  <  1:461968/135‑2 (MQ=255)

                                                                                                                              gATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGATAACTACAAGCATTGCAGGAAAAAGATATAGa  <  1:324731/135‑1 (MQ=255)

                                                                                                                              gATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAGa  <  1:225599/135‑1 (MQ=255)

                                                                                                                              gATACTTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAGa  <  1:578265/135‑1 (MQ=255)

TTACAATTATCCAAATGAATATTTGTTAACTAATGTCAAAATTCCTAAAAGAAGAAAAACAATAGAGGATATCGAAAAAGATGAATCTAAAATGTACAACTATTTAGAAATGAACCAAGTCCTACAGATACGTGATCATATACTAAATGATAATAAGTTACACAAGCGAAATCGCATTTTAATTGCCAGCATCTTAGAAGTACAGGCTTTAACTGGTATGCGCATAGGAGAACTACAAGCACTGCAGGAAAAAGATATAGA  >  USA300TCH1516_ALE/1605144‑1605404

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A