BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236064.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 = 1,942,488 number of mapped reads = 1,608,102 (82.79%) number of supplementary alignments = 12,718 (0.65%) number of secondary alignments = 0 number of mapped bases = 105,110,866 bp number of sequenced bases = 105,051,292 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 114,805 duplication rate = 5.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0885 >>>>>>> ACTG content number of A's = 29,137,871 bp (27.74%) number of C's = 18,211,219 bp (17.34%) number of T's = 34,607,087 bp (32.94%) number of G's = 23,048,702 bp (21.94%) number of N's = 46,413 bp (0.04%) GC percentage = 39.28% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 912,416 number of insertions = 7,920 mapped reads with insertion percentage = 0.49% number of deletions = 34,360 mapped reads with deletion percentage = 2.11% homopolymer indels = 45.46% >>>>>>> Coverage mean coverageData = 0.034X std coverageData = 0.4237X There is a 2.6% of reference with a coverageData >= 1X There is a 0.55% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% 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 9173872 0.03680581401640721 0.9204333976510415 chr2 243199373 8521567 0.03503942832944722 0.3786551962534916 chr3 198022430 16036805 0.08098479046035341 0.35651686256421217 chr4 191154276 4362837 0.022823643244056963 0.22671171569237147 chr5 180915260 8050616 0.04449937501126218 0.2646353719579264 chr6 171115067 8394785 0.04905929762456277 0.398685145898656 chr7 159138663 4464672 0.028055231304789836 0.3372255278762155 chr8 146364022 7902431 0.05399162234008573 0.7659372206072413 chr9 141213431 5214257 0.036924653434700555 0.3373137851328438 chr10 135534747 5102506 0.03764721676870065 0.39292299298763467 chr11 135006516 5550163 0.04111033425971825 0.354477109555564 chr12 133851895 2248845 0.016800994860775038 0.17115557208206508 chr13 115169878 2340030 0.020318073098939984 0.17453251360915356 chr14 107349540 3198841 0.02979836709127957 0.22398732280178912 chr15 102531392 2290104 0.0223356374601839 0.18622659889128132 chr16 90354753 1177421 0.013031090904537142 0.16967199395756122 chr17 81195210 1562099 0.019238807313879724 0.19103773116505995 chr18 78077248 1612444 0.02065190617374219 0.604303589747978 chr19 59128983 1638106 0.027703943428216922 0.4785260149565853 chr20 63025520 1177151 0.01867737069047586 0.17473771625564574 chr21 48129895 1194118 0.024810317994668388 0.2167327324761335 chr22 51304566 1572952 0.030659103519168254 0.21308683869599931 chrMT 16571 17345 1.0467081045199444 1.351355269720704 chrX 155270560 2043387 0.013160170221579674 0.16345186725120894 chrY 59373566 263512 0.00443820403174032 0.14445794115457755