BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008674.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 = 1,754,215 number of mapped reads = 1,236,337 (70.48%) number of supplementary alignments = 5,297 (0.3%) number of secondary alignments = 0 number of mapped bases = 77,609,226 bp number of sequenced bases = 77,562,501 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 142,996 duplication rate = 9.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.06 >>>>>>> ACTG content number of A's = 20,498,253 bp (26.43%) number of C's = 13,624,345 bp (17.57%) number of T's = 25,216,196 bp (32.51%) number of G's = 18,209,849 bp (23.48%) number of N's = 13,858 bp (0.02%) GC percentage = 41.04% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 673,932 number of insertions = 6,314 mapped reads with insertion percentage = 0.51% number of deletions = 28,843 mapped reads with deletion percentage = 2.3% homopolymer indels = 49.67% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2763X There is a 1.67% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 6472859 0.02596927933030105 0.40772993731747464 chr2 243199373 6566801 0.02700171846248962 0.3036393327064833 chr3 198022430 5225022 0.0263860109180561 0.23032895786960902 chr4 191154276 4327910 0.02264092695472844 0.22166460982338532 chr5 180915260 4245761 0.02346823037481747 0.21438545226955785 chr6 171115067 4385494 0.025628917878984907 0.24217536416175836 chr7 159138663 4604864 0.028936173731709685 0.3507871062598555 chr8 146364022 3754880 0.025654392033583225 0.2691799874006138 chr9 141213431 3221682 0.022814274656353332 0.2590301123587058 chr10 135534747 5027275 0.03709214877569366 0.3515341057992052 chr11 135006516 3532406 0.02616470748715566 0.284705893207366 chr12 133851895 4110504 0.03070934483221175 0.2517600833954775 chr13 115169878 2259966 0.01962289132580309 0.19936348749473182 chr14 107349540 2078292 0.019360045697447797 0.20609344729191745 chr15 102531392 1768849 0.01725177982563623 0.1845197743901355 chr16 90354753 2366260 0.026188550368789122 0.25854367460553324 chr17 81195210 1909670 0.023519490866517865 0.22941699686956288 chr18 78077248 1876223 0.02403034236042746 0.3824014315690011 chr19 59128983 1148525 0.019424061462379624 0.290340275217556 chr20 63025520 1501457 0.023823000587698442 0.22132793331766 chr21 48129895 974339 0.020243946096287973 0.21008721627399057 chr22 51304566 742323 0.014468946097312274 0.16606590341353572 chrMT 16571 65727 3.966387061734355 3.459206438309239 chrX 155270560 5206987 0.03353492767721067 0.2703233189506981 chrY 59373566 235150 0.003960516705363461 0.09568512630227338