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
A1 F169 I1 R1	62	44.4	970160	98.1%	951726	147.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	USA300TCH1516_ALE	1,163,829	T→C	V72A (GTG→GCG)	USA300HOU_RS05765 →	Putative metallophosphoesterase MG207

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	1,163,829	0	T	C	97.7%	152.1 / NA	43	V72A (GTG→GCG)	USA300HOU_RS05765	Putative metallophosphoesterase MG207
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (22/20); minor base G (0/1); total (22/21)
Fisher's exact test for biased strand distribution p-value = 4.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCCAGATGCAGATGTATATTTACATTTAGGAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGTGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGTTGTTTGTTTGCA‑TTTTATGGACATACACATGTGGCAAAATATGAGTATATTAATGGTG  >  USA300TCH1516_ALE/1163686‑1163969

cccAGATGCAGATGTATATTTACATTTAGGAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGaaa                                                                                                                                           >  3:77158/1‑148 (MQ=255)

 ccAGATGCAGATGTATATTTACATTTAGGAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAg                                                                                                                                          <  4:197531/148‑1 (MQ=255)

 ccAGATGCAGATGTATATTTACATTTAGGAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAg                                                                                                                                          >  3:141503/1‑148 (MQ=255)

    gatgcagatgTATATTTACATTTAGGAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCAt                                                                                                                                       <  4:273820/148‑1 (MQ=255)

    gatgcagatgTATATTTACATTTAGGAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCAt                                                                                                                                       <  3:102999/148‑1 (MQ=255)

    aatgcagatgTATATTTACATTTATTAGATTCAGAATTCGCGTATGAGGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCAt                                                                                                                                       <  4:36414/147‑1 (MQ=255)

                  tttACATTTAGGAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATAc                                                                                                                                >  1:56795/1‑141 (MQ=255)

                  tttACATTTAGGAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGAGGTCGCAAAATATAATGACGCGAAAGCATTTTATAc                                                                                                                                >  1:16371/1‑141 (MQ=255)

                     aCATTTAGGAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACAt                                                                                                                      >  3:47611/1‑148 (MQ=255)

                        tttAGGAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTta                                                                                                                   >  3:361455/1‑148 (MQ=255)

                        tttAGGAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTta                                                                                                                   >  4:266548/1‑148 (MQ=255)

                            ggAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACAt                                                                                                                      >  2:51567/1‑141 (MQ=255)

                            ggAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACAt                                                                                                                      >  1:45226/1‑141 (MQ=255)

                            ggAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATc                                                                                                               >  4:374480/1‑148 (MQ=255)

                              agaTTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCaa                                                                                                             >  4:383080/1‑148 (MQ=255)

                               gaTTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAg                                                                                                            >  4:304103/1‑148 (MQ=255)

                               gaTTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAg                                                                                                            >  3:299417/1‑148 (MQ=255)

                               gaTTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAg                                                                                                            >  3:299419/1‑148 (MQ=255)

                                           gcgTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACaa                                                                                                <  3:291430/148‑1 (MQ=255)

                                             gTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAaga                                                                                              >  4:121366/1‑148 (MQ=255)

                                             gTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAaga                                                                                              >  4:387367/1‑148 (MQ=255)

                                             gTATGATGATACGGAACTTAGCTTATTAAATAGAGTAAAAGGCAATTGTGAATTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCACTTTATACTCATGGACATTTATATCAAGTCAATCGAACaaca                                                                                              >  4:147021/1‑146 (MQ=255)

                                                                 gCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAgg                                                                          <  4:71527/148‑1 (MQ=255)

                                                                           tAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGGAAAAGGACTTGAATTa                                                                >  3:335448/1‑148 (MQ=255)

                                                                           tAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTa                                                                >  3:397956/1‑148 (MQ=255)

                                                                               gTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGgtt                                                            >  4:112580/1‑148 (MQ=255)

                                                                                  aaaGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTa                                                                >  1:30144/1‑141 (MQ=255)

                                                                                     ggCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGttgtttgt                                                      <  3:362121/148‑1 (MQ=255)

                                                                                     ggCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGttgtttgt                                                      <  3:234426/148‑1 (MQ=255)

                                                                                     ggCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGttgtttgt                                                      <  3:19985/148‑1 (MQ=255)

                                                                                     ggCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCAGAAAAAGGACTTGAATTAGGttgtttgt                                                      <  4:135111/148‑1 (MQ=255)

                                                                                     ggCAATTGTGATTATTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATATAAAAAAAAAAAAAGGACTTGAATTAGGttgtttgt                                                      <  4:160358/148‑1 (MQ=255)

                                                                                                  tttACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGTTGTTTGTTTGCA‑TTTTATgg                                        <  3:101299/148‑1 (MQ=255)

                                                                                                  tttACCCAGAATTTGAAAAAGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGTTGTTTGTTTGCA‑TTTTATgg                                        <  3:101313/148‑1 (MQ=255)

                                                                                                             tttGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGTTGTTTGTTTGCA‑TTTTATGGACAt                                    <  2:66796/141‑1 (MQ=255)

                                                                                                             tttGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGTTGTTTGTTTGCA‑TTTTATGGACATACACAtg                             <  4:143160/148‑1 (MQ=255)

                                                                                                             tttGAAAATGAAGCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGTTGTTTGTTTGCA‑TTTTATGGACATACACAtg                             <  3:240869/148‑1 (MQ=255)

                                                                                                                         gCGGTCGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGTTGTTTGTTTGCA‑TTTTATGGACATACACATGTGGCAAAATATg                 <  3:383080/148‑1 (MQ=255)

                                                                                                                              cGCAAAATATAATGACGCGAAAGCATTTTATACTCATGGAAATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGATTTGAATTAGGTTGTTTGTTTGCA‑TTTTATGGACATACACATGTGGCAAAata                   <  2:14313/141‑1 (MQ=255)

                                                                                                                                     tataATGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGTTGTTTGTTTGCA‑TTTTATGGACATACACATGTGGCAAAATATGAGTATATTAATg     >  3:51246/1‑148 (MQ=255)

                                                                                                                                       taATGACGGGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGTTGTTTGTTTGCA‑TTTTATGGACATACACATGTGGCAAAATATGAGTatat          <  2:56795/141‑1 (MQ=255)

                                                                                                                                        aaTGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAATAAGAGATAAAAAAAAAAAAAAAGGACTTGAATTAGGTTGTTTGTTTGCA‑TTTTATGGACATACACATGTGGCAAAATATGAGTATATTAATGgtg  <  4:51158/148‑1 (MQ=255)

                                                                                                                                         aTGACGCGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGTTGTTTGTTTGCATTTTTATGGACATACACATGTGGCAAAATATGAGTATAtt         <  2:26349/141‑1 (MQ=255)

CCCAGATGCAGATGTATATTTACATTTAGGAGATTCAGAATTCGCGTATGATGATACGGAACTTAGCTTATTTAATAGAGTAAAAGGCAATTGTGATTTTTACCCAGAATTTGAAAATGAAGCGGTCGCAAAATATAATGACGTGAAAGCATTTTATACTCATGGACATTTATATCAAGTCAATCGAACAAGAGATTTATTAGCTGAAAAAGGACTTGAATTAGGTTGTTTGTTTGCA‑TTTTATGGACATACACATGTGGCAAAATATGAGTATATTAATGGTG  >  USA300TCH1516_ALE/1163686‑1163969

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A