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	129,796	G→C	intergenic (‑209/+212)	spa ← / ← sarS	Immunoglobulin G‑binding protein A/HTH‑type transcriptional regulator SarS

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	USA300TCH1516_ALE	129,796	0	G	C	97.6%	152.4 / NA	42	intergenic (‑209/+212)	spa/sarS	Immunoglobulin G‑binding protein A/HTH‑type transcriptional regulator SarS
Reads supporting (aligned to +/- strand): ref base G (0/0); major base C (17/24); minor base T (0/1); total (17/25)
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

CTATATTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGAGATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAGTTGTT  >  USA300TCH1516_ALE/129657‑129928

cTATATTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATAttttt                                                                                                                              >  4:180439/1‑148 (MQ=255)

cTATATTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATAttttt                                                                                                                              >  3:283332/1‑148 (MQ=255)

    atTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATAtt                                                                                                                                 <  1:13724/141‑1 (MQ=255)

     tttATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATaa                                                                                                                         <  4:268428/148‑1 (MQ=255)

         aaaTTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGaa                                                                                                                     <  4:122406/147‑1 (MQ=255)

           aTTAAATTTTAAGGTAAGTTTTACAACTTATAAAATAAGTTTTTTGCAGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCACTTAATCTCGCTATTTCGATTAATAAAACCAGATAAAATATAGATATATTTTTtata                                                                                                                          <  2:22799/141‑1 (MQ=255)

           aTTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGCAAGATTTAGTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTtata                                                                                                                          <  2:14427/141‑1 (MQ=255)

           aTTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAg                                                                                                                   >  4:374935/1‑148 (MQ=255)

           aTTAAATTTAAAGGTAAGTTTTACAACTTATAAAAGAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATCTGGACATGTTTTTtata                                                                                                                          <  2:15079/141‑1 (MQ=255)

             tAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGACAGCg                                                                                                                 >  4:82490/1‑148 (MQ=255)

              aaaTTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCgg                                                                                                                <  3:73014/148‑1 (MQ=255)

                    aaaGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATAAAAGCg                                                                                                                 >  2:63022/1‑141 (MQ=255)

                     aaGGTAAGTTTTACACCTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGCAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATa                                                                                                         >  4:288158/1‑148 (MQ=255)

                     aaGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATa                                                                                                         >  4:327161/1‑148 (MQ=255)

                      aGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATAc                                                                                                        <  4:127498/148‑1 (MQ=255)

                          aaGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACatat                                                                                                    <  3:88091/148‑1 (MQ=255)

                            gTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGa                                                                                                  <  3:395779/148‑1 (MQ=255)

                            gTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGa                                                                                                  <  3:169245/148‑1 (MQ=255)

                                                         cTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTgg                                                                     <  4:376536/148‑1 (MQ=255)

                                                         cTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTgg                                                                     <  3:212773/148‑1 (MQ=255)

                                                         cTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTgg                                                                     >  4:273521/1‑148 (MQ=255)

                                                         cTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGCTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTgg                                                                     >  3:326715/1‑148 (MQ=255)

                                                              aGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCtt                                                                >  4:1406/1‑148 (MQ=255)

                                                                    aTTCAGGAAGTAAAAGGCTTCAAAACGCAAAATCACGCTATTTAGATTAATAAAAACAGATAAAAAATAGACATATTTTTTATAATGAGAGCGGTTAAATACATAAGAATCAAACAATATTTTACAAAATAAAGTAGGGCt                                                                 >  2:1516/1‑141 (MQ=255)

                                                                         ggAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTg                                                     >  3:334027/1‑148 (MQ=255)

                                                                          gAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGa                                                    >  4:298083/1‑148 (MQ=255)

                                                                                             cGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATgg                                 <  4:284799/148‑1 (MQ=255)

                                                                                              gCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGt                                <  3:180439/148‑1 (MQ=255)

                                                                                              gCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGt                                <  4:283332/148‑1 (MQ=255)

                                                                                                   aTCACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTaa                           <  3:206394/148‑1 (MQ=255)

                                                                                                     cACGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGt                         <  3:356227/148‑1 (MQ=255)

                                                                                                      aCGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTg                        <  3:160112/148‑1 (MQ=255)

                                                                                                      aCGCTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGCGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTg                        <  3:300269/148‑1 (MQ=255)

                                                                                                         cTATTTCGATTAATAACAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGata                     >  3:366153/1‑148 (MQ=255)

                                                                                                         cTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGata                     >  4:8733/1‑148 (MQ=255)

                                                                                                         cTATTTCGATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGata                     >  4:404533/1‑148 (MQ=255)

                                                                                                                gATTAATAAAAACAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTAAGGTTTAATTTCGGAAATGGTTTTAAGTGata                     >  2:22536/1‑141 (MQ=255)

                                                                                                                           aCAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAgttgt   <  4:283227/148‑1 (MQ=255)

                                                                                                                           aCAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAgttgt   <  4:117326/148‑1 (MQ=255)

                                                                                                                            cAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAgttgtt  <  3:298864/148‑1 (MQ=255)

                                                                                                                            cAGATAAAATATAGACATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAgttgtt  <  4:89799/148‑1 (MQ=255)

                                                                                                                            cAGATAAAATATAGACATAATTTTTATAATGAAAGCGGTTTAATAAAAAAAAAAAAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAgttgtt  <  4:56664/148‑1 (MQ=255)

CTATATTTATAATTAAATTTAAAGGTAAGTTTTACAACTTATAAAATAAATATTTTGCTGAAAGATTTATTCAGGAAGTAAAAGGCTTAAAACCGCAAAATCACGCTATTTCGATTAATAAAAACAGATAAAATATAGAGATATTTTTTATAATGAAAGCGGTTTAATACATATGAGTTAAAAAATATTTTTAAGAATAAAGTGGGGCTTTGAATGTGCTGAGGTTTAATTTCGGAAATGGTTTTAAGTGATATAGAAAATAGAAAGTTGTT  >  USA300TCH1516_ALE/129657‑129928

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