BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472580.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 7,371,370 number of mapped reads = 6,720,702 (91.17%) number of supplementary alignments = 218,787 (2.97%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,390,882 number of mapped paired reads (second in pair) = 3,329,820 number of mapped paired reads (both in pair) = 6,545,968 number of mapped paired reads (singletons) = 174,734 number of mapped bases = 543,688,119 bp number of sequenced bases = 543,456,208 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 993,186 duplication rate = 12.88% >>>>>>> Insert size mean insert size = 257,971.5918 std insert size = 4,913,032.7942 median insert size = 128 >>>>>>> Mapping quality mean mapping quality = 50.3071 >>>>>>> ACTG content number of A's = 140,057,261 bp (25.77%) number of C's = 108,394,790 bp (19.95%) number of T's = 162,136,352 bp (29.83%) number of G's = 132,504,682 bp (24.38%) number of N's = 363,123 bp (0.07%) GC percentage = 44.33% >>>>>>> Mismatches and indels general error rate = 0.0122 number of mismatches = 6,547,912 number of insertions = 52,138 mapped reads with insertion percentage = 0.76% number of deletions = 124,118 mapped reads with deletion percentage = 1.81% homopolymer indels = 42.43% >>>>>>> Coverage mean coverageData = 0.1756X std coverageData = 1.7744X There is a 10.21% of reference with a coverageData >= 1X There is a 4.31% of reference with a coverageData >= 2X There is a 1.35% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 35457467 0.14225628348584937 2.155325637516116 chr2 243199373 54483955 0.22402999780760124 2.38880303889805 chr3 198022430 28744903 0.14515983366126756 0.5503838480369991 chr4 191154276 27898670 0.14594844846682897 0.9370921584243045 chr5 180915260 26359462 0.14570060038053176 0.5838567342321827 chr6 171115067 36462662 0.21308855286250158 1.0229522383142995 chr7 159138663 46381949 0.29145619377234555 3.2752809652335304 chr8 146364022 27096465 0.18513063955020312 1.6065514198472284 chr9 141213431 18365926 0.1300579262888953 1.8713421148537173 chr10 135534747 21450366 0.15826469945747565 1.5873674513773823 chr11 135006516 19762987 0.14638543075950497 1.3436171434124307 chr12 133851895 27339298 0.20425036193921647 0.6806812269223632 chr13 115169878 26142661 0.22699217411691622 0.7264929266527022 chr14 107349540 13737518 0.12796997546519528 4.303881879406974 chr15 102531392 12593618 0.12282694845301623 0.5142467219095468 chr16 90354753 19579465 0.21669546260615644 0.9672335622484436 chr17 81195210 19666628 0.24221414046468998 1.305887183485572 chr18 78077248 12223122 0.15655164997618767 3.183222219022874 chr19 59128983 11195177 0.18933484785287108 1.5567512483880517 chr20 63025520 18860919 0.29925844324648176 1.088003198829135 chr21 48129895 8124394 0.168801407108825 0.757219965527737 chr22 51304566 5634742 0.10982924989561357 0.4973583191394576 chrMT 16571 227321 13.718001327620541 9.843054668180269 chrX 155270560 24698626 0.1590683127567776 0.8619922601510622 chrY 59373566 1199818 0.02020794910650979 0.6989878828434374