BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173921.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 6,655,464 number of mapped reads = 6,473,305 (97.26%) number of supplementary alignments = 614,194 (9.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,239,455 number of mapped paired reads (second in pair) = 3,233,850 number of mapped paired reads (both in pair) = 6,354,430 number of mapped paired reads (singletons) = 118,875 number of mapped bases = 765,730,391 bp number of sequenced bases = 765,323,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,085,298 duplication rate = 65.46% >>>>>>> Insert size mean insert size = 878,633.8277 std insert size = 8,464,703.8848 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 52.7503 >>>>>>> ACTG content number of A's = 230,944,496 bp (30.18%) number of C's = 149,632,120 bp (19.55%) number of T's = 230,239,539 bp (30.08%) number of G's = 154,498,522 bp (20.19%) number of N's = 9,280 bp (0%) GC percentage = 39.74% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 7,745,325 number of insertions = 77,486 mapped reads with insertion percentage = 1.15% number of deletions = 158,308 mapped reads with deletion percentage = 2.38% homopolymer indels = 43.44% >>>>>>> Coverage mean coverageData = 0.2474X std coverageData = 3.567X There is a 4.86% of reference with a coverageData >= 1X There is a 3.89% of reference with a coverageData >= 2X There is a 3.05% of reference with a coverageData >= 3X There is a 2.55% of reference with a coverageData >= 4X There is a 1.98% of reference with a coverageData >= 5X There is a 1.62% of reference with a coverageData >= 6X There is a 1.23% of reference with a coverageData >= 7X There is a 1.01% of reference with a coverageData >= 8X There is a 0.76% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.48% of reference with a coverageData >= 11X There is a 0.41% of reference with a coverageData >= 12X There is a 0.31% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.2% of reference with a coverageData >= 15X There is a 0.18% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.12% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% 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 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% 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 70318310 0.2821188959043757 1.8987307469920556 chr2 243199373 56261665 0.2313396794818217 10.490670867715576 chr3 198022430 46517798 0.23491176226854704 1.4363269700770827 chr4 191154276 48311061 0.25273335240483974 1.9526728099312969 chr5 180915260 39616243 0.2189767905703477 1.3812006213777546 chr6 171115067 37394029 0.21853148092447056 1.4463291957390345 chr7 159138663 67709011 0.4254717849426698 4.039663889889547 chr8 146364022 76865131 0.5251641076110903 2.7804172296704714 chr9 141213431 26828622 0.18998633352375668 1.6086080453062435 chr10 135534747 34060488 0.2513044717602933 4.401712364574635 chr11 135006516 31793945 0.2354993369357076 1.467947529531254 chr12 133851895 29421235 0.21980439649360212 1.3941571081939979 chr13 115169878 19987814 0.1735507091533083 1.2388212143594275 chr14 107349540 25433304 0.23692047492704674 1.450459053811002 chr15 102531392 17879444 0.17438019372642477 1.2099352176491 chr16 90354753 17280097 0.19124723853763398 1.7382466729191013 chr17 81195210 18313777 0.22555243098700034 1.5563414323658034 chr18 78077248 13614407 0.17437098961274863 2.032241291110296 chr19 59128983 9458970 0.1599718026606343 1.3625015563205491 chr20 63025520 29066905 0.4611926248287995 2.0587613438402257 chr21 48129895 8739594 0.1815834836124201 1.423030536396967 chr22 51304566 7607524 0.1482816168837682 1.09465191801754 chrMT 16571 1991839 120.20028966266369 88.32249754189684 chrX 155270560 29869117 0.1923681926567406 1.3127755373648347 chrY 59373566 1390061 0.02341211912385387 1.095029595839969