BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975199.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP029757/SRP029757.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 = 2,530,024 number of mapped reads = 2,503,957 (98.97%) number of supplementary alignments = 22,966 (0.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,253,717 number of mapped paired reads (second in pair) = 1,250,240 number of mapped paired reads (both in pair) = 2,495,600 number of mapped paired reads (singletons) = 8,357 number of mapped bases = 342,089,036 bp number of sequenced bases = 341,866,916 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 376,162 duplication rate = 14.51% >>>>>>> Insert size mean insert size = 72,158.1485 std insert size = 2,567,769.2588 median insert size = 175 >>>>>>> Mapping quality mean mapping quality = 53.7231 >>>>>>> ACTG content number of A's = 100,092,676 bp (29.28%) number of C's = 69,166,217 bp (20.23%) number of T's = 100,689,875 bp (29.45%) number of G's = 71,899,185 bp (21.03%) number of N's = 18,963 bp (0.01%) GC percentage = 41.26% >>>>>>> Mismatches and indels general error rate = 0.0118 number of mismatches = 3,906,550 number of insertions = 56,744 mapped reads with insertion percentage = 2.19% number of deletions = 128,472 mapped reads with deletion percentage = 4.96% homopolymer indels = 49.29% >>>>>>> Coverage mean coverageData = 0.1105X std coverageData = 1.4167X There is a 6.21% of reference with a coverageData >= 1X There is a 3.38% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 30347338 0.12175431249978712 1.9065379261188207 chr2 243199373 24466233 0.10060154636994069 1.2434673982630478 chr3 198022430 27436695 0.13855347093761045 0.5507805352687581 chr4 191154276 19078714 0.09980793733329826 0.6533477285020077 chr5 180915260 31849430 0.1760461223669026 0.6058695229000308 chr6 171115067 17604295 0.10287986504426287 0.7119641284428936 chr7 159138663 15130547 0.09507775618298364 0.8553602695900134 chr8 146364022 18214273 0.12444501559269805 0.630208989850639 chr9 141213431 12403937 0.08783822411339896 1.7441769083170688 chr10 135534747 17004092 0.1254592816704044 4.559267994473959 chr11 135006516 13473801 0.09980111626612155 0.921896781814022 chr12 133851895 12710780 0.0949615244520819 0.4297608769044552 chr13 115169878 7214653 0.06264357595308037 0.3465000661673266 chr14 107349540 10516469 0.09796473277854753 0.4530996790765038 chr15 102531392 8068421 0.07869220189656646 0.39203544344914737 chr16 90354753 9901721 0.10958716250378107 2.1183001189604185 chr17 81195210 5856236 0.072125387692205 1.1726693980917264 chr18 78077248 8446581 0.10818236062828444 1.6614681115196195 chr19 59128983 4199313 0.07101953706864872 1.0358692899689 chr20 63025520 5594131 0.0887597754052644 0.4558916960653276 chr21 48129895 3901835 0.08106884504942302 0.4962732138709034 chr22 51304566 2628286 0.051229085535973544 0.318377140859705 chrMT 16571 25347 1.5295999034457788 1.7429840125862153 chrX 155270560 35110250 0.22612303323952718 0.949284896098598 chrY 59373566 905658 0.01525355576587736 0.9402083282380658