BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008684.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 = 1,436,588 number of mapped reads = 1,261,029 (87.78%) number of supplementary alignments = 6,913 (0.48%) number of secondary alignments = 0 number of mapped bases = 81,245,185 bp number of sequenced bases = 81,194,773 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,527 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.1796 >>>>>>> ACTG content number of A's = 21,677,557 bp (26.7%) number of C's = 15,181,727 bp (18.7%) number of T's = 25,060,677 bp (30.86%) number of G's = 19,240,391 bp (23.7%) number of N's = 34,421 bp (0.04%) GC percentage = 42.39% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 707,241 number of insertions = 5,762 mapped reads with insertion percentage = 0.45% number of deletions = 28,793 mapped reads with deletion percentage = 2.25% homopolymer indels = 43.64% >>>>>>> Coverage mean coverageData = 0.0262X std coverageData = 0.3415X There is a 2.39% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 7450012 0.0298896426821741 0.7275568151348297 chr2 243199373 7062696 0.029040765660197653 0.384242526478493 chr3 198022430 6214031 0.03138044008448942 0.20896232339504556 chr4 191154276 4224222 0.02209849598132976 0.1638431892034661 chr5 180915260 3452695 0.01908459794933827 0.14907162646589184 chr6 171115067 3820965 0.022329798696218844 0.18615602318044833 chr7 159138663 4641635 0.02916723637423044 0.4103860124309085 chr8 146364022 6554035 0.04477900313507373 0.3453471565657605 chr9 141213431 2091410 0.014810276793005617 0.266371831709712 chr10 135534747 5020594 0.037042855143264476 0.5400615522518042 chr11 135006516 3651153 0.02704427244089463 0.2900582097170844 chr12 133851895 3380655 0.02525668388930915 0.1720157931181071 chr13 115169878 2000150 0.017366954230862344 0.13778403483224483 chr14 107349540 3381570 0.031500554170982006 0.1947239936809212 chr15 102531392 1961856 0.019134198431637404 0.14934652194319742 chr16 90354753 2141204 0.023697746149557844 0.21228031443021417 chr17 81195210 2521769 0.03105810059485036 0.23623321742290973 chr18 78077248 1083704 0.01387989494711699 0.44194029462222617 chr19 59128983 1679226 0.028399372267234834 0.49624040726436863 chr20 63025520 1982588 0.03145690824922984 0.19323927878514022 chr21 48129895 752378 0.015632238549450398 0.14244257613953487 chr22 51304566 1106020 0.021557925273161846 0.15444823533029903 chrMT 16571 6137 0.3703457848047794 0.6459909969722345 chrX 155270560 4823095 0.031062520802398085 0.22318598067204184 chrY 59373566 241385 0.004065529767910521 0.11921012473551093