BamQC report ----------------------------------- >>>>>>> Input bam file = SRR8617731.sorted.bam outfile = /mainsd2/zhouyj/SRP186739/SRP186739.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 = 36,333,562 number of mapped reads = 35,004,184 (96.34%) number of supplementary alignments = 1,371,230 (3.77%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 17,799,885 number of mapped paired reads (second in pair) = 17,204,299 number of mapped paired reads (both in pair) = 34,189,666 number of mapped paired reads (singletons) = 814,518 number of mapped bases = 4,718,699,796 bp number of sequenced bases = 4,714,862,194 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,076,424 duplication rate = 15.93% >>>>>>> Insert size mean insert size = 276,411.2736 std insert size = 5,059,363.0183 median insert size = 277 >>>>>>> Mapping quality mean mapping quality = 52.8328 >>>>>>> ACTG content number of A's = 1,365,394,641 bp (28.96%) number of C's = 919,043,510 bp (19.49%) number of T's = 1,390,327,906 bp (29.49%) number of G's = 1,040,077,389 bp (22.06%) number of N's = 18,748 bp (0%) GC percentage = 41.55% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 64,387,719 number of insertions = 943,480 mapped reads with insertion percentage = 2.49% number of deletions = 1,864,032 mapped reads with deletion percentage = 5.08% homopolymer indels = 44.06% >>>>>>> Coverage mean coverageData = 1.5243X std coverageData = 19.9116X There is a 36.64% of reference with a coverageData >= 1X There is a 25.51% of reference with a coverageData >= 2X There is a 18.31% of reference with a coverageData >= 3X There is a 13.61% of reference with a coverageData >= 4X There is a 10.25% of reference with a coverageData >= 5X There is a 7.84% of reference with a coverageData >= 6X There is a 6.05% of reference with a coverageData >= 7X There is a 4.72% of reference with a coverageData >= 8X There is a 3.71% of reference with a coverageData >= 9X There is a 2.94% of reference with a coverageData >= 10X There is a 2.35% of reference with a coverageData >= 11X There is a 1.88% of reference with a coverageData >= 12X There is a 1.52% of reference with a coverageData >= 13X There is a 1.23% of reference with a coverageData >= 14X There is a 1.01% of reference with a coverageData >= 15X There is a 0.83% of reference with a coverageData >= 16X There is a 0.68% of reference with a coverageData >= 17X There is a 0.57% of reference with a coverageData >= 18X There is a 0.47% of reference with a coverageData >= 19X There is a 0.4% of reference with a coverageData >= 20X There is a 0.33% of reference with a coverageData >= 21X There is a 0.28% of reference with a coverageData >= 22X There is a 0.24% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.15% of reference with a coverageData >= 26X There is a 0.13% of reference with a coverageData >= 27X There is a 0.12% of reference with a coverageData >= 28X There is a 0.1% of reference with a coverageData >= 29X There is a 0.09% of reference with a coverageData >= 30X There is a 0.08% of reference with a coverageData >= 31X There is a 0.07% of reference with a coverageData >= 32X There is a 0.07% of reference with a coverageData >= 33X There is a 0.06% of reference with a coverageData >= 34X There is a 0.05% of reference with a coverageData >= 35X There is a 0.05% of reference with a coverageData >= 36X There is a 0.05% of reference with a coverageData >= 37X There is a 0.04% of reference with a coverageData >= 38X There is a 0.04% of reference with a coverageData >= 39X There is a 0.04% of reference with a coverageData >= 40X There is a 0.03% of reference with a coverageData >= 41X There is a 0.03% of reference with a coverageData >= 42X There is a 0.03% of reference with a coverageData >= 43X There is a 0.03% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.02% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 405784999 1.6280200120343933 23.381293532302898 chr2 243199373 415363766 1.7079146252568669 25.578768144516268 chr3 198022430 368214611 1.8594591077384517 3.8848241078961214 chr4 191154276 284774170 1.4897609196040167 19.75861144108047 chr5 180915260 280197315 1.5487765653378271 3.826358445063198 chr6 171115067 292020180 1.7065719876087826 12.06136561919526 chr7 159138663 241540331 1.5177979156454269 21.77394668103945 chr8 146364022 205767111 1.4058585449366785 5.57062241607384 chr9 141213431 201236561 1.4250525575007096 31.7136883035114 chr10 135534747 239314645 1.765706951885925 51.296916432687325 chr11 135006516 216996880 1.6073067169587578 16.16252618675967 chr12 133851895 202478333 1.5127042691476278 6.792616577643489 chr13 115169878 190515841 1.6542158792596793 3.440184381410201 chr14 107349540 133313298 1.2418618468230045 3.767187028953491 chr15 102531392 125566910 1.2246679534010423 4.389075654212167 chr16 90354753 139770669 1.5469099782719786 27.962240485393398 chr17 81195210 111401651 1.372022450585447 15.423494926968027 chr18 78077248 103447628 1.3249394753257697 24.567555241893455 chr19 59128983 60034276 1.0153104781118931 11.58647871500016 chr20 63025520 95987062 1.522987228030804 6.6644642871021516 chr21 48129895 58560665 1.2167212290822575 9.87112450819296 chr22 51304566 45827401 0.8932421531448098 3.559835567145283 chrMT 16571 2517851 151.9432140486392 69.36826762876564 chrX 155270560 278534356 1.7938645677583696 7.525672661635186 chrY 59373566 19533286 0.328989604565776 25.704998983675402