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
A22 F68 I1 R1	31	72.2	3191514	95.4%	3044704	126.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	BS168_reference_genome	1,684,164	A→C	Q168H (CAA→CAC)	topA →	DNA topoisomerase I

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	BS168_reference_genome	1,684,164	0	A	C	97.1%	114.0 / ‑3.9	35	Q168H (CAA→CAC)	topA	DNA topoisomerase I
Reads supporting (aligned to +/- strand): ref base A (1/0); new base C (18/15); total (19/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.74e-01

CCCCGCATGATCAATATGGATTTAGTGGATGCACAGCAAGCGAGACGTATTTTAGACAGGCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCAATCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACTTTAAGCCTGAGGAATATTGGACAATTGACGGTACGTTCTTAAAAGGTCAAGAAACCTTTGAAGCGAGCTTTTTCGGGAAAAACG  >  BS168_reference_genome/1684033‑1684297

ccccGCATGATCAATATGGATTTAGTGGATGCACAGCAAGCGAGACGTATTTTAGACAGGCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTg                                                                                                                                >  4:110165/1‑139 (MQ=255)

 cccGCATGATCAATATGGATTTAGTGGATGCACAGCAAGCGAGACGTATTTTAGACAGGCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGc                                                                                                                               >  6:368647/1‑139 (MQ=255)

  ccGCATGATCAATATGGATTTAGTGGATGCACAGCAAGCGAGACGTATTTTAGACAGGCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGcc                                                                                                                              <  6:178333/139‑1 (MQ=255)

       tGATCAATATGGATTTAGTGGATGCACAGCAAGCGAGACGTATTTTAGACAGGCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCg                                                                                                                         <  1:392480/139‑1 (MQ=255)

            aaTATGGATTTAGTGGATGCACAGCAAGCGAGACTTATTTTAGACAGGCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTTTg                                                                                                                     <  5:68683/138‑1 (MQ=255)

                   aTTTAGTGGATGCACAGCAAGCGAGACGTATTTTAGACAGGCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGtt                                                                                                                       >  3:329191/1‑129 (MQ=255)

                   aTTTAGTGGATGCACAGCAAGCGAGACGTATTTTAGACAGGCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGtt                                                                                                                       <  4:329191/129‑1 (MQ=255)

                             tgtacaGCAAGCGAGACGTATTTTAGACAGGCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGAAGGACGCGTGCACTCCGTTGCCCTCCGTTTGAGTATTGACCGTGaaa                                                                                                     >  8:105605/4‑137 (MQ=255)

                                      cgctagaCTTATTTTAGACAGGATTGGCGGATATAAAATCAGTCCAATCTTATGTAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTTTTATTATTGACCGTGAAAAAGAGATTAAc                                                                                          <  1:124238/135‑1 (MQ=255)

                                      aGCGTGACGTATTTTTGACTGGCTTGTCGTATATAAAATAAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGATTAGCGCAGGACGGGTGCACTCCGTTGCCCTCGGTTTTATTATTGACCGTGAAAAAGAGATTAAc                                                                                          <  5:399959/139‑1 (MQ=255)

                                             cGTATTTTAGACAGGCTTGCCGTATAAAAAATCAGTCCAATCTTATGCAAAAAAGCCAAAACCGGGCTACCCCCCGCCCGCGTGCACGCCGTTGCCCTCCGTTTGATTATTCCCCGTCAAAAAGAGATAAACGACTTTa                                                                                   <  2:144537/139‑1 (MQ=255)

                                                      gACAGGCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTTTTATTATTGACCGTGAAAAAGACATTAACGACTTTAAGCCTGAg                                                                           <  3:110165/138‑1 (MQ=255)

                                                        cAGGCTTGTGGTAAATAAAATCATTCAAATCTTATGGAAAAAAGTAAAAAAAGGGCTTTGCGCAGGACGCGTGCACTCGGTTGCCCTCCGTTTTATTATTGACCGTTAAAATTATATAAACGACTTTAAGCCTGAGGaa                                                                        <  6:67432/139‑1 (MQ=255)

                                                         aGGCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTGTGATTATTGACCGGGAAAAAGAGATTAACGGCTTTAAGCCGGAGGaa                                                                        >  2:184290/1‑138 (MQ=255)

                                                          ggCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCTGGACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGa                                                                                                             >  1:139329/1‑100 (MQ=255)

                                                          ggCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGa                                                                                                             <  2:139329/100‑1 (MQ=255)

                                                           gCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGACCGTg                                                                                                        <  8:256518/104‑1 (MQ=255)

                                                           gCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGACCGTg                                                                                                        >  7:256518/1‑104 (MQ=255)

                                                           gCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACTTTAAGCCTGAGGAatat                                                                     >  5:67432/1‑139 (MQ=255)

                                                           gCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACTTTAAGCCTGAGGAatat                                                                     >  7:53781/1‑139 (MQ=255)

                                                                     tataAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAag                                                                                                  <  7:113870/100‑1 (MQ=255)

                                                                     tataAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAag                                                                                                  >  8:113870/1‑100 (MQ=255)

                                                                                          ttgAAAAAATGCAAAAAAGGGCTTCGCGCAGGACGCGGGCAGTCCGTTGCCCTGCGTTTGATTTTTGCCCGTTAAAAAGAGATTAACGACTTTAAGCCTGAGGAATATTGGACAATTGACGGTACGTTCTTAAAAGGt                                       <  6:94095/136‑1 (MQ=255)

                                                                                          tGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCATCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACTTTAAGCCTGAGGAATATTGGACAATTGACGGTACGTTCTTAAAAGGt                                       >  6:133572/1‑138 (MQ=255)

                                                                                              aaaaaGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCGGTTGCCCTCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACTTTAAGCCTGAGGAATATTGGACAATTGACGGTACGTTCTTAAAAGGTCAAGa                                  <  5:368647/139‑1 (MQ=255)

                                                                                               aaaaGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGtt                                                                                                                       >  7:214753/1‑53 (MQ=255)

                                                                                               aaaaGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGtt                                                                                                                       <  8:214753/53‑1 (MQ=255)

                                                                                               aaaaGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACATTAAGCCTGAGGAATATTGGACAAGTGACGGTACGTTCTTAAAAGGTCAAGa                                  >  5:94095/1‑138 (MQ=255)

                                                                                                         aaaGGCCTTAGCGCAGGACGCGGTCACGCCGTGGCCCTCAGTTGTATTATTCACCTTTAAAAAGTGATTTACGACTTTAAGCCTGAGGAATATTGGACAATTGACGGTACGTTCTTAAAAGTTCAAGAAACCTTTGAAg                       <  8:365887/139‑1 (MQ=255)

                                                                                                              gCTTAGCGCAGGACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACTTTAAGCCTGAGGAATATTGGACAATTGACGGTACGTTCTTAAAAGGTCAAGAAACCTTTGAAGCGAGc                  >  7:182635/1‑139 (MQ=255)

                                                                                                                        ggACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACTTTAAGCCTGAGGAATATTGGACAATTGACGGTACGTTCTTAAAAGGTCAAGAAACCTTTGAAGCGAGCTTTTTCggg         >  5:107800/1‑138 (MQ=255)

                                                                                                                        ggACGCGTGCAATCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACTTTAAGCCTGAGGAATATTGGACAATTGACGGTACGTTCTTAAAAGGTCAAGAAACCTTTGAAGCGAGCTTTTTCggg         >  2:113139/1‑138 (MQ=255)

                                                                                                                         gACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACTTTAAGCCTGAGGAATATTGGACAATTGACGGTACGTTCTTAAAAGGTCAAGAAACCTTTGAAGCGAGCTTTTTCGGGa        >  5:98194/1‑138 (MQ=255)

                                                                                                                         gACGCGTGCACTCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACTTTAAGCCTGAGGAATATTGGACAATTGACGGTACGTTCTTAAAAGGTCAAGAAACCTTTGAAGCGAGCTTTTTCGGGa        >  1:90356/1‑138 (MQ=255)

                                                                                                                              gTGCACTCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACTTTAAGCCTGAGGAATATTGGACAATTGACGGTACGTTCTTAAAAGGTCAAGAAACCTTTGAAGCGAGCTTTTTCGGGAAAAACg  >  4:372519/1‑139 (MQ=255)

CCCCGCATGATCAATATGGATTTAGTGGATGCACAGCAAGCGAGACGTATTTTAGACAGGCTTGTCGGATATAAAATCAGTCCAATCTTATGGAAAAAAGTCAAAAAAGGGCTTAGCGCAGGACGCGTGCAATCCGTTGCCCTCCGTTTGATTATTGACCGTGAAAAAGAGATTAACGACTTTAAGCCTGAGGAATATTGGACAATTGACGGTACGTTCTTAAAAGGTCAAGAAACCTTTGAAGCGAGCTTTTTCGGGAAAAACG  >  BS168_reference_genome/1684033‑1684297

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A