BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238305.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 = 1,481,371 number of mapped reads = 1,328,414 (89.67%) number of supplementary alignments = 20,941 (1.41%) number of secondary alignments = 0 number of mapped bases = 87,195,520 bp number of sequenced bases = 87,154,618 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,934 duplication rate = 6.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0631 >>>>>>> ACTG content number of A's = 24,267,346 bp (27.84%) number of C's = 16,484,392 bp (18.91%) number of T's = 27,178,653 bp (31.18%) number of G's = 19,202,988 bp (22.03%) number of N's = 21,239 bp (0.02%) GC percentage = 40.95% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 705,455 number of insertions = 6,570 mapped reads with insertion percentage = 0.49% number of deletions = 23,863 mapped reads with deletion percentage = 1.77% homopolymer indels = 46.15% >>>>>>> Coverage mean coverageData = 0.0282X std coverageData = 0.2815X There is a 2.02% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 11975716 0.04804688530745927 0.32657538256066876 chr2 243199373 2485909 0.010221691648851413 0.24960313730659978 chr3 198022430 3492343 0.017636098092524165 0.17737443334092423 chr4 191154276 3640207 0.01904329359600619 0.19729007528886217 chr5 180915260 6482538 0.03583190273722626 0.2537796189089191 chr6 171115067 3494340 0.02042099542292205 0.2007031834489507 chr7 159138663 2857395 0.017955378951499675 0.27172191043205424 chr8 146364022 8449923 0.05773224105579717 0.4791784000131448 chr9 141213431 3123486 0.02211890170701964 0.2772797186082609 chr10 135534747 1662212 0.012264102282199265 0.2180305594283178 chr11 135006516 7938099 0.058797895354917536 0.4699002527195212 chr12 133851895 3409966 0.025475664726300664 0.21870434927616758 chr13 115169878 2516306 0.021848646917903308 0.19477106497288316 chr14 107349540 1524931 0.014205286766948419 0.18686533194063712 chr15 102531392 6180188 0.0602760567222183 0.3246561530128432 chr16 90354753 2186969 0.024204249664652396 0.22811188186326728 chr17 81195210 2604626 0.03207856719626687 0.2600350609298655 chr18 78077248 1799730 0.023050633137069586 0.46513904829667624 chr19 59128983 1224515 0.020709218015807915 0.2708129618912375 chr20 63025520 1002733 0.015909952032129207 0.17041553204644444 chr21 48129895 672905 0.013981019489030674 0.18299899655156518 chr22 51304566 2064286 0.040235911945926996 0.265132944720664 chrMT 16571 7778 0.469374207953654 0.9694863678511948 chrX 155270560 6130650 0.03948366000612093 0.2828626052398738 chrY 59373566 267769 0.004509902605479348 0.1803017774180304