BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173999.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 2,436,248 number of mapped reads = 2,393,866 (98.26%) number of supplementary alignments = 304,252 (12.49%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,195,711 number of mapped paired reads (second in pair) = 1,198,155 number of mapped paired reads (both in pair) = 2,365,222 number of mapped paired reads (singletons) = 28,644 number of mapped bases = 282,545,201 bp number of sequenced bases = 282,457,727 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,990,571 duplication rate = 70.08% >>>>>>> Insert size mean insert size = 1,126,085.023 std insert size = 10,375,144.7578 median insert size = 155 >>>>>>> Mapping quality mean mapping quality = 53.0664 >>>>>>> ACTG content number of A's = 84,717,426 bp (29.99%) number of C's = 56,195,325 bp (19.9%) number of T's = 84,219,559 bp (29.82%) number of G's = 57,321,877 bp (20.29%) number of N's = 3,540 bp (0%) GC percentage = 40.19% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 2,124,668 number of insertions = 22,739 mapped reads with insertion percentage = 0.93% number of deletions = 38,072 mapped reads with deletion percentage = 1.56% homopolymer indels = 45.96% >>>>>>> Coverage mean coverageData = 0.0913X std coverageData = 1.4572X There is a 1.65% of reference with a coverageData >= 1X There is a 1.42% of reference with a coverageData >= 2X There is a 1.1% of reference with a coverageData >= 3X There is a 0.96% of reference with a coverageData >= 4X There is a 0.74% of reference with a coverageData >= 5X There is a 0.64% of reference with a coverageData >= 6X There is a 0.48% of reference with a coverageData >= 7X There is a 0.41% of reference with a coverageData >= 8X There is a 0.31% of reference with a coverageData >= 9X There is a 0.27% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.18% of reference with a coverageData >= 12X There is a 0.13% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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 23742487 0.09525547781884965 0.9482946140238195 chr2 243199373 24610609 0.1011951992162414 4.012347060755585 chr3 198022430 21556696 0.10885987006623442 1.0258383974949885 chr4 191154276 16757628 0.08766546242470663 0.9317237862007975 chr5 180915260 17200789 0.09507649603466285 0.9541018380848696 chr6 171115067 15332741 0.08960485636253177 0.94695211261162 chr7 159138663 19525512 0.1226949606834387 1.1077286919915172 chr8 146364022 20477788 0.139909984162638 1.4750652397744177 chr9 141213431 10707802 0.07582707908286712 0.833765727814097 chr10 135534747 12151386 0.08965513470874004 0.9758001683606422 chr11 135006516 11484063 0.08506302762453333 0.8949978429625057 chr12 133851895 11334216 0.0846772920174197 0.8934641400518092 chr13 115169878 7997765 0.06944320111201299 0.8185958819304174 chr14 107349540 8796328 0.08194099387850194 0.8838994707333684 chr15 102531392 8057916 0.07858974547034336 0.8549833815390672 chr16 90354753 8249684 0.09130326547403654 0.938007049572177 chr17 81195210 8053157 0.09918266114466605 0.9698087554867906 chr18 78077248 5081747 0.06508614391736758 0.7943562197215971 chr19 59128983 3771318 0.0637812086164242 0.7435625750864016 chr20 63025520 10747553 0.17052700239522023 1.2817286770610479 chr21 48129895 3370081 0.07002053505414878 0.8247256671555271 chr22 51304566 2475973 0.048260285449057305 0.6609004865116845 chrMT 16571 487304 29.407036388872125 46.589585814873566 chrX 155270560 10191286 0.06563566203406493 0.7936093335553696 chrY 59373566 383372 0.006456947524425264 0.2247756935518184