BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716576.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,461,341 number of mapped reads = 1,317,753 (90.17%) number of supplementary alignments = 7,335 (0.5%) number of secondary alignments = 0 number of mapped bases = 76,157,376 bp number of sequenced bases = 76,135,030 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 42,036 duplication rate = 2.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2525 >>>>>>> ACTG content number of A's = 20,027,299 bp (26.3%) number of C's = 14,736,755 bp (19.36%) number of T's = 22,788,796 bp (29.93%) number of G's = 18,581,268 bp (24.41%) number of N's = 912 bp (0%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 381,215 number of insertions = 6,248 mapped reads with insertion percentage = 0.47% number of deletions = 14,283 mapped reads with deletion percentage = 1.08% homopolymer indels = 40.68% >>>>>>> Coverage mean coverageData = 0.0246X std coverageData = 0.2415X There is a 2.23% of reference with a coverageData >= 1X There is a 0.16% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 6401153 0.025681592985880665 0.3462999188250864 chr2 243199373 7621434 0.03133821401751723 0.3158726816915413 chr3 198022430 5529780 0.027925018393118395 0.18473422481278745 chr4 191154276 4277583 0.022377647466280064 0.17359474913601913 chr5 180915260 4113258 0.022735826706934505 0.16185124077175098 chr6 171115067 4246477 0.02481649964815781 0.17996777886244303 chr7 159138663 3828998 0.02406076517056072 0.44615016960948 chr8 146364022 5391717 0.03683772095303585 0.2683811738351122 chr9 141213431 3538327 0.025056589695069444 0.18863565228465465 chr10 135534747 3731783 0.027533773313495765 0.3036657317293352 chr11 135006516 2291169 0.01697080309812602 0.17400477016517257 chr12 133851895 3414135 0.025506811091467924 0.18333099023107985 chr13 115169878 1992933 0.01730429027631687 0.14070496430356766 chr14 107349540 2451535 0.022836939962667748 0.1649115344829071 chr15 102531392 1862194 0.018162183928996108 0.14699745165740424 chr16 90354753 2392957 0.026484019053209077 0.18106899760395118 chr17 81195210 2836435 0.03493352625111752 0.20702936373973532 chr18 78077248 1856809 0.023781691178459567 0.2823508860993011 chr19 59128983 1613200 0.027282728674700864 0.2958062514048188 chr20 63025520 1733654 0.02750717487138543 0.1852220055392043 chr21 48129895 814089 0.01691441462733297 0.14930601280265196 chr22 51304566 1288317 0.025111156773063824 0.17132422225720959 chrMT 16571 104099 6.2819986723794585 4.401554578732074 chrX 155270560 2647642 0.017051796554350032 0.15631034243478234 chrY 59373566 177698 0.0029928807038472308 0.08737978211974422