BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525114.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 = 699,899 number of mapped reads = 622,969 (89.01%) number of supplementary alignments = 15,958 (2.28%) number of secondary alignments = 0 number of mapped bases = 47,137,273 bp number of sequenced bases = 47,119,280 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,854 duplication rate = 1.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9798 >>>>>>> ACTG content number of A's = 12,598,488 bp (26.74%) number of C's = 8,921,627 bp (18.93%) number of T's = 14,803,001 bp (31.42%) number of G's = 10,794,399 bp (22.91%) number of N's = 1,765 bp (0%) GC percentage = 41.84% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 361,035 number of insertions = 4,184 mapped reads with insertion percentage = 0.67% number of deletions = 10,642 mapped reads with deletion percentage = 1.69% homopolymer indels = 42.88% >>>>>>> Coverage mean coverageData = 0.0152X std coverageData = 0.1869X There is a 1.42% of reference with a coverageData >= 1X There is a 0.07% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 4636472 0.018601646733710644 0.2942969034321393 chr2 243199373 4077836 0.016767460991768263 0.23989220404618136 chr3 198022430 3139750 0.015855527073372445 0.1313340746669204 chr4 191154276 3076359 0.01609359238189367 0.1355166010555749 chr5 180915260 2858830 0.015802039031975523 0.13240148254257839 chr6 171115067 2714492 0.01586354753903699 0.14149344493487034 chr7 159138663 2632656 0.016543157711460726 0.2592179734849232 chr8 146364022 1373742 0.00938579017731557 0.2159287691675616 chr9 141213431 1980484 0.014024756611146995 0.1776053451153721 chr10 135534747 2213660 0.01633278586486755 0.18784881395644137 chr11 135006516 2648300 0.019616090233748423 0.21980876978386307 chr12 133851895 2137823 0.015971555725826668 0.1329467154266246 chr13 115169878 1458601 0.012664778545654098 0.11761283170281348 chr14 107349540 1429955 0.013320550791368086 0.13153141326676995 chr15 102531392 1313174 0.012807531180304272 0.11852108200162213 chr16 90354753 1038933 0.011498376847978324 0.1178614948318021 chr17 81195210 1366457 0.016829280939109584 0.15092297798936608 chr18 78077248 1314300 0.01683332896159455 0.2772785749587489 chr19 59128983 873016 0.014764603680059912 0.21118743947050517 chr20 63025520 908860 0.014420507756223194 0.1262584421116884 chr21 48129895 608900 0.012651180726656478 0.12251296147330189 chr22 51304566 473359 0.009226449747182347 0.1001841740059003 chrMT 16571 2694 0.16257316999577576 0.4439515587816413 chrX 155270560 2755024 0.01774337646492677 0.16725789033026736 chrY 59373566 103596 0.001744816876924657 0.05237957657825936