BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038394.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 14,506,684 number of mapped reads = 14,158,927 (97.6%) number of supplementary alignments = 220,451 (1.52%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 7,148,094 number of mapped paired reads (second in pair) = 7,010,833 number of mapped paired reads (both in pair) = 14,003,888 number of mapped paired reads (singletons) = 155,039 number of mapped bases = 2,035,657,426 bp number of sequenced bases = 2,034,141,337 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,234,452 duplication rate = 10.13% >>>>>>> Insert size mean insert size = 78,035.1446 std insert size = 2,661,136.1786 median insert size = 253 >>>>>>> Mapping quality mean mapping quality = 53.8073 >>>>>>> ACTG content number of A's = 607,631,368 bp (29.87%) number of C's = 403,251,485 bp (19.82%) number of T's = 607,482,594 bp (29.86%) number of G's = 415,734,509 bp (20.44%) number of N's = 41,381 bp (0%) GC percentage = 40.26% >>>>>>> Mismatches and indels general error rate = 0.0145 number of mismatches = 28,342,001 number of insertions = 395,925 mapped reads with insertion percentage = 2.61% number of deletions = 766,532 mapped reads with deletion percentage = 5.18% homopolymer indels = 47.13% >>>>>>> Coverage mean coverageData = 0.6576X std coverageData = 9.3433X There is a 25.44% of reference with a coverageData >= 1X There is a 14.33% of reference with a coverageData >= 2X There is a 7.89% of reference with a coverageData >= 3X There is a 4.85% of reference with a coverageData >= 4X There is a 2.94% of reference with a coverageData >= 5X There is a 1.87% of reference with a coverageData >= 6X There is a 1.2% of reference with a coverageData >= 7X There is a 0.79% of reference with a coverageData >= 8X There is a 0.53% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.26% of reference with a coverageData >= 11X There is a 0.19% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.11% of reference with a coverageData >= 14X There is a 0.08% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 124145464 0.4980748433120253 8.120024663723628 chr2 243199373 230957663 0.9496638916087995 14.212090871609144 chr3 198022430 133125760 0.6722761658868645 1.5608582004962217 chr4 191154276 106034484 0.554706314809301 7.232745778284399 chr5 180915260 125186236 0.691960622890518 1.7449891826745396 chr6 171115067 146043567 0.8534816340866115 13.751184812640316 chr7 159138663 146071337 0.9178871698827833 10.033600080502888 chr8 146364022 91583792 0.6257261227762654 2.8654716537121274 chr9 141213431 83494043 0.5912613439723025 16.197858746355166 chr10 135534747 81245087 0.5994410200950167 18.712218132548 chr11 135006516 115036813 0.8520834135146484 7.225293523628509 chr12 133851895 62304873 0.465476211599395 1.349627394028901 chr13 115169878 122257303 1.0615388773790313 2.118611794901971 chr14 107349540 36871188 0.34346852347946716 1.3018196283989782 chr15 102531392 34404469 0.3355505892283214 1.0217033679320386 chr16 90354753 77447613 0.8571504035875125 15.465681710657377 chr17 81195210 42525121 0.5237392821571617 5.524871008058959 chr18 78077248 33773606 0.4325665525506227 13.23391128021502 chr19 59128983 24485699 0.41410654737626723 5.16961286111141 chr20 63025520 58532974 0.9287186206476361 2.884691219656895 chr21 48129895 18738699 0.3893359626070242 3.7051312585279086 chr22 51304566 10493261 0.20452879379195996 1.0464214099319953 chrMT 16571 849506 51.264618912558085 35.54109492467394 chrX 155270560 103184387 0.6645457258607169 2.3030943984308716 chrY 59373566 26864481 0.4524653445945962 12.892486490894695