BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063590.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,191,351 number of mapped reads = 4,604,259 (88.69%) number of supplementary alignments = 34,287 (0.66%) number of secondary alignments = 0 number of mapped bases = 305,417,521 bp number of sequenced bases = 305,288,481 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 309,663 duplication rate = 5.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.6945 >>>>>>> ACTG content number of A's = 84,616,400 bp (27.72%) number of C's = 57,727,931 bp (18.91%) number of T's = 94,338,009 bp (30.9%) number of G's = 68,298,679 bp (22.37%) number of N's = 307,462 bp (0.1%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 2,500,006 number of insertions = 21,261 mapped reads with insertion percentage = 0.46% number of deletions = 74,274 mapped reads with deletion percentage = 1.6% homopolymer indels = 46.44% >>>>>>> Coverage mean coverageData = 0.0987X std coverageData = 0.7981X There is a 7.25% of reference with a coverageData >= 1X There is a 1.74% of reference with a coverageData >= 2X There is a 0.47% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 26039577 0.1044714628815308 1.4732308485686203 chr2 243199373 24563025 0.10099954081707274 0.9080720065639043 chr3 198022430 24275439 0.12258934000557412 0.4458232946219332 chr4 191154276 21658834 0.11330551663934528 0.453901371457625 chr5 180915260 13742103 0.07595878313415905 0.35683396365580516 chr6 171115067 15985996 0.09342249212922904 0.44547055822586873 chr7 159138663 21586943 0.13564863869693314 1.4753257736192735 chr8 146364022 17768435 0.12139892548183734 1.1126933684441702 chr9 141213431 8428204 0.059684152848038935 0.6424330747662093 chr10 135534747 14383562 0.10612453498732691 0.6860075818928556 chr11 135006516 11738303 0.08694619598953283 0.5374539851752941 chr12 133851895 14055085 0.10500475170710134 0.4290850553012417 chr13 115169878 9760328 0.08474722878494323 0.37934536407366576 chr14 107349540 9702540 0.0903826881791948 0.43852094509732026 chr15 102531392 6943432 0.06772005982323931 0.345164567500957 chr16 90354753 8255519 0.09136784425718036 0.4515228824968949 chr17 81195210 7699889 0.094831813354507 0.4565760397277121 chr18 78077248 8194546 0.10495433957918189 1.4422928361467529 chr19 59128983 5747434 0.09720163798521615 0.9977096639119317 chr20 63025520 8527166 0.13529703523271208 0.5172680525113171 chr21 48129895 3139502 0.06522977039530213 0.35937749228346993 chr22 51304566 4044628 0.07883563423965033 0.3563142055639344 chrMT 16571 51692 3.1194255023836823 3.0081306594706745 chrX 155270560 18397139 0.11848439910308818 0.5170069771086164 chrY 59373566 728200 0.01226471726491887 0.18954111372336335