BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085052.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 3,164,433 number of mapped reads = 2,892,673 (91.41%) number of supplementary alignments = 41,603 (1.31%) number of secondary alignments = 0 number of mapped bases = 200,056,268 bp number of sequenced bases = 199,984,595 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,406 duplication rate = 3.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.7317 >>>>>>> ACTG content number of A's = 60,555,440 bp (30.28%) number of C's = 41,016,175 bp (20.51%) number of T's = 58,984,635 bp (29.49%) number of G's = 39,405,730 bp (19.7%) number of N's = 22,615 bp (0.01%) GC percentage = 40.21% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,795,236 number of insertions = 13,740 mapped reads with insertion percentage = 0.47% number of deletions = 41,622 mapped reads with deletion percentage = 1.43% homopolymer indels = 47.51% >>>>>>> Coverage mean coverageData = 0.0646X std coverageData = 0.4809X There is a 4.8% of reference with a coverageData >= 1X There is a 1.11% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 20265389 0.08130526984725145 0.5844835324786797 chr2 243199373 20246560 0.08325087252589257 0.583027516363476 chr3 198022430 12141838 0.061315468151764425 0.3187617809926594 chr4 191154276 12036858 0.06296933687217125 0.3275447324900551 chr5 180915260 10626855 0.0587394065044596 0.3118773708858009 chr6 171115067 14139974 0.08263430127985165 0.5253195743787153 chr7 159138663 18119719 0.11386119914806624 0.5770230091077719 chr8 146364022 12074883 0.0824989832542317 1.0492618255770636 chr9 141213431 4588681 0.03249464988921628 0.35751126955134405 chr10 135534747 11080444 0.08175352996379592 0.5300363557815707 chr11 135006516 9520222 0.0705167593540448 0.5567240369132355 chr12 133851895 7848572 0.058636241197780575 0.3165930538903473 chr13 115169878 4017371 0.03488213298272314 0.23726250047894776 chr14 107349540 6580965 0.061304081973709436 0.3331643632945237 chr15 102531392 3465161 0.0337960982720297 0.2622020731740735 chr16 90354753 4665781 0.051638467762730754 0.30143889186224215 chr17 81195210 2943089 0.036247076644053265 0.3005863739820764 chr18 78077248 5820687 0.07455036068894232 0.6152032527301722 chr19 59128983 2808832 0.047503472197382456 0.4610891768926555 chr20 63025520 4686212 0.07435419810895649 0.3532950494105176 chr21 48129895 2798134 0.05813713077911348 0.3175414360217005 chr22 51304566 1111414 0.021663062114198568 0.18297644075328978 chrMT 16571 16503 0.9958964455977309 1.3452321962037477 chrX 155270560 8104889 0.052198491459037696 0.33434024713664007 chrY 59373566 347235 0.005848309666965262 0.11771456313137403