BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525018.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 = 1,043,350 number of mapped reads = 958,889 (91.9%) number of supplementary alignments = 3,930 (0.38%) number of secondary alignments = 0 number of mapped bases = 55,582,232 bp number of sequenced bases = 55,564,992 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 22,614 duplication rate = 1.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1115 >>>>>>> ACTG content number of A's = 14,096,959 bp (25.37%) number of C's = 10,455,840 bp (18.82%) number of T's = 16,800,187 bp (30.24%) number of G's = 14,211,444 bp (25.58%) number of N's = 562 bp (0%) GC percentage = 44.39% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 268,486 number of insertions = 3,311 mapped reads with insertion percentage = 0.34% number of deletions = 10,302 mapped reads with deletion percentage = 1.07% homopolymer indels = 42.94% >>>>>>> Coverage mean coverageData = 0.018X std coverageData = 0.1844X There is a 1.67% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 6129001 0.02458971205532122 0.32594392097908764 chr2 243199373 5013350 0.02061415676429396 0.20867279280605847 chr3 198022430 3157599 0.015945663327129152 0.13366011117467078 chr4 191154276 3649254 0.019090621859800823 0.1523149604925996 chr5 180915260 2472756 0.013668034415670629 0.12429137777656854 chr6 171115067 3351233 0.019584675147279695 0.1849289230902599 chr7 159138663 3644806 0.02290333430789223 0.24501709416453504 chr8 146364022 3413793 0.02332399009915155 0.18742184108702387 chr9 141213431 1614302 0.011431646328315613 0.13748114596179278 chr10 135534747 2927554 0.021600025563924208 0.19099635965364248 chr11 135006516 2423525 0.017951170593869706 0.16919707736165066 chr12 133851895 3107000 0.02321222273319328 0.16010823339101182 chr13 115169878 1111966 0.009655007188598394 0.10451443380830794 chr14 107349540 1309003 0.01219383893028326 0.11846287089356435 chr15 102531392 1603550 0.015639600406478438 0.13439381796389382 chr16 90354753 1304003 0.014432035468017936 0.13243227166789312 chr17 81195210 1482682 0.01826070774372035 0.17413371872641895 chr18 78077248 1157125 0.014820258521406901 0.21880246996326644 chr19 59128983 1461129 0.024710876559469998 0.21905440378358754 chr20 63025520 1083286 0.017188053347279006 0.13870524656210398 chr21 48129895 832756 0.017302260892112897 0.142713609461489 chr22 51304566 790027 0.015398765872027842 0.13011595352939256 chrMT 16571 4450 0.26854142779554646 0.5314893028313815 chrX 155270560 2385698 0.015364780032995308 0.144020333063861 chrY 59373566 152384 0.00256652935415737 0.07473725248037759