BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524863.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,973,949 number of mapped reads = 1,808,668 (91.63%) number of supplementary alignments = 8,732 (0.44%) number of secondary alignments = 0 number of mapped bases = 104,931,367 bp number of sequenced bases = 104,900,670 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,838 duplication rate = 2.18% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7565 >>>>>>> ACTG content number of A's = 26,564,501 bp (25.32%) number of C's = 18,182,855 bp (17.33%) number of T's = 34,968,233 bp (33.33%) number of G's = 25,171,294 bp (24%) number of N's = 13,787 bp (0.01%) GC percentage = 41.33% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 508,662 number of insertions = 7,576 mapped reads with insertion percentage = 0.42% number of deletions = 19,624 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.5% >>>>>>> Coverage mean coverageData = 0.0339X std coverageData = 0.3302X There is a 3.06% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% 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 8753737 0.03512022142564692 0.6489440177809828 chr2 243199373 6760660 0.02779883811624794 0.3506527325382378 chr3 198022430 7515598 0.03795326620322759 0.2105589044207554 chr4 191154276 5656824 0.029592976512856035 0.19920523517994604 chr5 180915260 6361555 0.035163175289911974 0.2043314213155868 chr6 171115067 6887004 0.0402477941933658 0.24164855803282942 chr7 159138663 4803459 0.030184110570289257 0.4678307534820004 chr8 146364022 11260527 0.07693507493255412 0.43397018627329276 chr9 141213431 4339295 0.030728628072212195 0.26966338028594394 chr10 135534747 5240951 0.03866868914434171 0.3089026483595218 chr11 135006516 5073555 0.0375800750239344 0.2879713880825951 chr12 133851895 4121793 0.030793684318029268 0.19535289902985278 chr13 115169878 2818459 0.024472188813120042 0.17033950903572706 chr14 107349540 2215900 0.020641914255058756 0.17042946235342957 chr15 102531392 3121059 0.03044003342898144 0.1905790173940961 chr16 90354753 3024088 0.033469052812307505 0.2141817389437206 chr17 81195210 2832526 0.03488538301705236 0.23331328626982614 chr18 78077248 2577006 0.03300585082097156 0.516202716366085 chr19 59128983 1552776 0.026260827114175125 0.4536819712797841 chr20 63025520 2241464 0.03556438725138642 0.20663199004044916 chr21 48129895 1512589 0.031427224181561166 0.20306151792659705 chr22 51304566 640136 0.01247717405893269 0.11869048155304822 chrMT 16571 15614 0.9422485064268904 1.071979093816973 chrX 155270560 5341585 0.03440178872285899 0.23626089772179906 chrY 59373566 263207 0.004433067065569213 0.1077888034286312