BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716500.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 = 702,035 number of mapped reads = 582,920 (83.03%) number of supplementary alignments = 3,392 (0.48%) number of secondary alignments = 0 number of mapped bases = 32,895,386 bp number of sequenced bases = 32,886,136 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,941 duplication rate = 1.02% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.854 >>>>>>> ACTG content number of A's = 7,843,234 bp (23.85%) number of C's = 6,694,740 bp (20.36%) number of T's = 9,999,513 bp (30.41%) number of G's = 8,348,184 bp (25.39%) number of N's = 465 bp (0%) GC percentage = 45.74% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 169,960 number of insertions = 2,012 mapped reads with insertion percentage = 0.34% number of deletions = 5,547 mapped reads with deletion percentage = 0.94% homopolymer indels = 39.08% >>>>>>> Coverage mean coverageData = 0.0106X std coverageData = 0.1288X There is a 1.02% of reference with a coverageData >= 1X There is a 0.03% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 2660012 0.010672037603469 0.17369955475196044 chr2 243199373 2730601 0.01122782911122061 0.16755025337204035 chr3 198022430 2143460 0.010824329344913099 0.1068405312354647 chr4 191154276 2060362 0.010778529484739332 0.1118071421301388 chr5 180915260 1938911 0.010717233029430463 0.10592002859115805 chr6 171115067 1865642 0.010902850536241791 0.1126717671114813 chr7 159138663 1821656 0.011446973134366474 0.16459718775588048 chr8 146364022 1639355 0.011200532600832737 0.12558722012482113 chr9 141213431 1369942 0.009701216026682334 0.11491090754123302 chr10 135534747 1587373 0.011711926536447514 0.14324197804860492 chr11 135006516 1455109 0.01077806496391626 0.1194599802394956 chr12 133851895 1512757 0.011301722698808261 0.10959531240379534 chr13 115169878 993312 0.00862475516384588 0.09501717992558181 chr14 107349540 1000444 0.009319499645736721 0.10172742538826424 chr15 102531392 949575 0.00926130994105688 0.09889480359433715 chr16 90354753 1013901 0.011221335528414316 0.11451992027207279 chr17 81195210 997483 0.012284998092867793 0.11797972946161454 chr18 78077248 851476 0.010905558556572076 0.17023873224561228 chr19 59128983 775839 0.013121128770302037 0.16123271398416322 chr20 63025520 709855 0.011262977282853042 0.10938142189609389 chr21 48129895 428221 0.008897193729593633 0.1002869732847132 chr22 51304566 425981 0.008302984182733366 0.09379445695543547 chrMT 16571 6036 0.36425079958964457 0.6617830478841035 chrX 155270560 1848006 0.011901844110048937 0.11826263995232891 chrY 59373566 110077 0.0018539731974326758 0.06025215170181316