BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5514765.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP106579/SRP106579.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 = 19,353,952 number of mapped reads = 7,440,920 (38.45%) number of supplementary alignments = 1,200,415 (6.2%) number of secondary alignments = 0 number of mapped bases = 679,864,163 bp number of sequenced bases = 679,326,803 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,032,853 duplication rate = 28.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2843 >>>>>>> ACTG content number of A's = 213,110,659 bp (31.37%) number of C's = 125,697,413 bp (18.5%) number of T's = 209,382,597 bp (30.82%) number of G's = 131,091,099 bp (19.3%) number of N's = 45,035 bp (0.01%) GC percentage = 37.8% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 3,895,716 number of insertions = 381,097 mapped reads with insertion percentage = 4.91% number of deletions = 183,657 mapped reads with deletion percentage = 2.31% homopolymer indels = 48.01% >>>>>>> Coverage mean coverageData = 0.2196X std coverageData = 12.4985X There is a 2.21% of reference with a coverageData >= 1X There is a 1.27% of reference with a coverageData >= 2X There is a 0.97% of reference with a coverageData >= 3X There is a 0.8% of reference with a coverageData >= 4X There is a 0.69% of reference with a coverageData >= 5X There is a 0.61% of reference with a coverageData >= 6X There is a 0.54% of reference with a coverageData >= 7X There is a 0.49% of reference with a coverageData >= 8X There is a 0.45% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.38% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.33% of reference with a coverageData >= 13X There is a 0.31% of reference with a coverageData >= 14X There is a 0.29% of reference with a coverageData >= 15X There is a 0.27% of reference with a coverageData >= 16X There is a 0.26% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.23% of reference with a coverageData >= 19X There is a 0.22% of reference with a coverageData >= 20X There is a 0.21% of reference with a coverageData >= 21X There is a 0.2% of reference with a coverageData >= 22X There is a 0.19% of reference with a coverageData >= 23X There is a 0.18% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.17% of reference with a coverageData >= 26X There is a 0.16% of reference with a coverageData >= 27X There is a 0.16% of reference with a coverageData >= 28X There is a 0.15% of reference with a coverageData >= 29X There is a 0.15% of reference with a coverageData >= 30X There is a 0.14% of reference with a coverageData >= 31X There is a 0.14% of reference with a coverageData >= 32X There is a 0.13% of reference with a coverageData >= 33X There is a 0.13% of reference with a coverageData >= 34X There is a 0.12% of reference with a coverageData >= 35X There is a 0.12% of reference with a coverageData >= 36X There is a 0.11% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.11% of reference with a coverageData >= 39X There is a 0.1% of reference with a coverageData >= 40X There is a 0.1% of reference with a coverageData >= 41X There is a 0.1% of reference with a coverageData >= 42X There is a 0.1% of reference with a coverageData >= 43X There is a 0.09% of reference with a coverageData >= 44X There is a 0.09% of reference with a coverageData >= 45X There is a 0.09% of reference with a coverageData >= 46X There is a 0.09% of reference with a coverageData >= 47X There is a 0.08% of reference with a coverageData >= 48X There is a 0.08% of reference with a coverageData >= 49X There is a 0.08% of reference with a coverageData >= 50X There is a 0.08% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 47342432 0.18993907341157637 5.177711349867057 chr2 243199373 69935058 0.2875626574908974 26.06176065035515 chr3 198022430 46147288 0.233040711600196 4.780367652307519 chr4 191154276 53348941 0.27908839978029054 5.775223564381905 chr5 180915260 39738693 0.219653626786375 4.604469250294397 chr6 171115067 49792807 0.29099019667274534 22.161134069945863 chr7 159138663 42602860 0.2677090481776889 7.418570249612492 chr8 146364022 35615364 0.2433341439605971 9.299910550588146 chr9 141213431 23210424 0.16436413898901728 3.90336028492659 chr10 135534747 25959707 0.19153543703446024 9.034860162647547 chr11 135006516 28185747 0.20877323432300113 4.230025885945155 chr12 133851895 42757669 0.31944014688772243 21.477889448644223 chr13 115169878 31608827 0.27445394185448385 4.6053903823252975 chr14 107349540 21168684 0.19719398890763762 3.3467391062197875 chr15 102531392 8950217 0.0872924557583301 2.2823887066642636 chr16 90354753 16749883 0.18537910230356117 12.839120683256292 chr17 81195210 8150073 0.1003762783543512 4.200256706936228 chr18 78077248 11317211 0.1449488972767073 2.9435369696725413 chr19 59128983 4098517 0.0693148569796981 2.3597118329639835 chr20 63025520 11612025 0.18424322401465312 8.312498844124937 chr21 48129895 7412183 0.15400372263434192 2.970367419644933 chr22 51304566 5045632 0.09834664618349953 22.28114417096535 chrMT 16571 14381819 867.890833383622 820.1201984908805 chrX 155270560 23866557 0.15370947976229363 14.478512879723214 chrY 59373566 10865545 0.1830030724447307 10.231893127669563