BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238656.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,710,309 number of mapped reads = 3,128,030 (84.31%) number of supplementary alignments = 24,544 (0.66%) number of secondary alignments = 0 number of mapped bases = 193,694,153 bp number of sequenced bases = 193,616,366 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,035,882 duplication rate = 21.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4731 >>>>>>> ACTG content number of A's = 47,725,166 bp (24.65%) number of C's = 34,158,410 bp (17.64%) number of T's = 65,025,249 bp (33.58%) number of G's = 46,703,119 bp (24.12%) number of N's = 4,422 bp (0%) GC percentage = 41.76% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,062,894 number of insertions = 12,642 mapped reads with insertion percentage = 0.4% number of deletions = 45,534 mapped reads with deletion percentage = 1.44% homopolymer indels = 41.77% >>>>>>> Coverage mean coverageData = 0.0626X std coverageData = 0.9721X There is a 2.31% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.37% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.18% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 21855679 0.08768555485364267 1.1119004969754862 chr2 243199373 18680761 0.07681253767048157 2.315638297886419 chr3 198022430 8486156 0.042854519056250345 0.49091422859502787 chr4 191154276 10489251 0.054873221878646336 0.5549809119618472 chr5 180915260 19661309 0.10867689657577807 0.7648748128064116 chr6 171115067 12575848 0.07349351650021561 0.8959795687661005 chr7 159138663 9344511 0.05871930066422639 0.8197619124875989 chr8 146364022 8014755 0.054759051373977685 0.6667016899710785 chr9 141213431 11138783 0.07887906214813235 0.7028175198245985 chr10 135534747 4929060 0.03636750065280308 0.5602124768626895 chr11 135006516 5712209 0.04231061706680884 0.4858961498884983 chr12 133851895 6607546 0.04936460555900236 0.5083262567035469 chr13 115169878 7949027 0.06902001754312877 0.7084795269052667 chr14 107349540 5300089 0.04937225627608651 0.5331384662308851 chr15 102531392 3463539 0.03378027872673376 0.5517190994935699 chr16 90354753 3603954 0.03988671188111156 0.4957904195797002 chr17 81195210 7805897 0.09613740761308456 0.7635541361136402 chr18 78077248 4579583 0.05865451354023134 1.8439615069735156 chr19 59128983 3186970 0.053898610094477696 0.8000651112954004 chr20 63025520 3660202 0.058074919492929214 0.6001179667554344 chr21 48129895 2708472 0.05627421377087982 0.5574854623839539 chr22 51304566 3022492 0.05891272913214001 0.5585629373327966 chrMT 16571 31412 1.8956007482952146 2.774576777844096 chrX 155270560 10342607 0.06661022540267775 0.6080974671096482 chrY 59373566 544041 0.00916301709080435 0.36364624413242863