BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174094.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 5,947,294 number of mapped reads = 5,821,052 (97.88%) number of supplementary alignments = 775,130 (13.03%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,911,558 number of mapped paired reads (second in pair) = 2,909,494 number of mapped paired reads (both in pair) = 5,740,630 number of mapped paired reads (singletons) = 80,422 number of mapped bases = 663,845,716 bp number of sequenced bases = 663,392,356 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,620,847 duplication rate = 64.35% >>>>>>> Insert size mean insert size = 1,024,480.5964 std insert size = 9,645,794.7268 median insert size = 157 >>>>>>> Mapping quality mean mapping quality = 52.6303 >>>>>>> ACTG content number of A's = 197,586,518 bp (29.78%) number of C's = 132,277,992 bp (19.94%) number of T's = 195,993,233 bp (29.54%) number of G's = 137,529,403 bp (20.73%) number of N's = 5,210 bp (0%) GC percentage = 40.67% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 5,573,297 number of insertions = 67,233 mapped reads with insertion percentage = 1.11% number of deletions = 196,778 mapped reads with deletion percentage = 3.3% homopolymer indels = 41.03% >>>>>>> Coverage mean coverageData = 0.2144X std coverageData = 3.8479X There is a 4.74% of reference with a coverageData >= 1X There is a 3.54% of reference with a coverageData >= 2X There is a 2.61% of reference with a coverageData >= 3X There is a 2.09% of reference with a coverageData >= 4X There is a 1.55% of reference with a coverageData >= 5X There is a 1.28% of reference with a coverageData >= 6X There is a 0.95% of reference with a coverageData >= 7X There is a 0.82% of reference with a coverageData >= 8X There is a 0.61% of reference with a coverageData >= 9X There is a 0.54% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.37% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.02% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 55032738 0.22079278189641902 1.722476488713923 chr2 243199373 62100981 0.25535008677838983 12.603564339286928 chr3 198022430 45999843 0.23229612423198726 1.4261033071801064 chr4 191154276 42235889 0.22095183996825685 1.5752618903774416 chr5 180915260 41337663 0.22849185303660952 1.4267561613023567 chr6 171115067 39136712 0.22871575651488363 1.5846244480729723 chr7 159138663 36834746 0.23146321142587456 1.6724576704690894 chr8 146364022 34912835 0.23853426902958433 2.135243272165729 chr9 141213431 28385572 0.20101184284659154 1.8330750272278309 chr10 135534747 32981817 0.24334584104842133 1.9026756829535927 chr11 135006516 29769146 0.22050154971779287 1.4287560907071395 chr12 133851895 31244277 0.2334242410240064 1.4937347202617879 chr13 115169878 21709542 0.1885001736304696 1.297986970726132 chr14 107349540 20318648 0.18927559447390274 1.304013476265302 chr15 102531392 19874983 0.1938429061803823 1.3322187078303032 chr16 90354753 19772738 0.2188345089051375 1.5007668614053282 chr17 81195210 18969203 0.233624655937216 1.4997276809229376 chr18 78077248 17641407 0.22594811487208155 2.4469175338116678 chr19 59128983 12677545 0.2144049222020274 1.5971151024162549 chr20 63025520 14401718 0.2285061352924974 1.4158771692559813 chr21 48129895 8835707 0.18358043374081742 1.4988715089878462 chr22 51304566 8576482 0.1671680060601234 1.3758453730302989 chrMT 16571 583833 35.23221290205781 33.10363734499252 chrX 155270560 16831392 0.10840040764971802 0.9726525203762947 chrY 59373566 3680299 0.0619854802051135 0.9348291810488499