BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10156409.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 = 7,638,424 number of mapped reads = 7,472,338 (97.83%) number of supplementary alignments = 1,039,750 (13.61%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,735,860 number of mapped paired reads (second in pair) = 3,736,478 number of mapped paired reads (both in pair) = 7,363,956 number of mapped paired reads (singletons) = 108,382 number of mapped bases = 844,612,775 bp number of sequenced bases = 844,027,377 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,060,930 duplication rate = 65.13% >>>>>>> Insert size mean insert size = 1,347,894.4278 std insert size = 10,984,157.7359 median insert size = 156 >>>>>>> Mapping quality mean mapping quality = 52.434 >>>>>>> ACTG content number of A's = 252,353,015 bp (29.9%) number of C's = 167,129,993 bp (19.8%) number of T's = 250,535,309 bp (29.68%) number of G's = 174,002,405 bp (20.62%) number of N's = 6,655 bp (0%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 7,076,810 number of insertions = 92,579 mapped reads with insertion percentage = 1.19% number of deletions = 244,787 mapped reads with deletion percentage = 3.19% homopolymer indels = 40.75% >>>>>>> Coverage mean coverageData = 0.2728X std coverageData = 5.1316X There is a 5.74% of reference with a coverageData >= 1X There is a 4.34% of reference with a coverageData >= 2X There is a 3.27% of reference with a coverageData >= 3X There is a 2.63% of reference with a coverageData >= 4X There is a 1.99% of reference with a coverageData >= 5X There is a 1.64% of reference with a coverageData >= 6X There is a 1.24% of reference with a coverageData >= 7X There is a 1.07% of reference with a coverageData >= 8X There is a 0.81% of reference with a coverageData >= 9X There is a 0.72% of reference with a coverageData >= 10X There is a 0.54% of reference with a coverageData >= 11X There is a 0.5% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.34% of reference with a coverageData >= 14X There is a 0.25% of reference with a coverageData >= 15X There is a 0.23% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.16% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.11% of reference with a coverageData >= 20X There is a 0.08% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% 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 0.02% of reference with a coverageData >= 31X There is a 0.02% 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 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% 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 63564963 0.2550242913938417 2.2354826279818543 chr2 243199373 85794511 0.3527743922267431 16.987542429004385 chr3 198022430 52173488 0.2634726177231539 1.5435444655529875 chr4 191154276 62489059 0.3269037988980168 2.4455976581376198 chr5 180915260 52493136 0.2901531689477162 1.637924012691327 chr6 171115067 52092622 0.30443036322453126 1.916166362750645 chr7 159138663 45249876 0.2843424416604531 2.200535037298606 chr8 146364022 43189820 0.29508494922338224 2.5162063374919716 chr9 141213431 36164494 0.2560981185989313 2.2203383055711248 chr10 135534747 44625872 0.3292577954197974 2.753223295407001 chr11 135006516 39211568 0.2904420405901001 1.714158531718406 chr12 133851895 34143930 0.25508738594997105 1.5854013718945588 chr13 115169878 28496419 0.2474294450498593 1.5233380393243896 chr14 107349540 24873715 0.2317076999118953 1.4723281013884937 chr15 102531392 23878020 0.23288496853724563 1.4797097545166986 chr16 90354753 25648618 0.28386573089298356 2.08989899862134 chr17 81195210 24285027 0.29909433081089387 1.7866669861684876 chr18 78077248 22852344 0.29268890214982984 2.9705632092065435 chr19 59128983 15104093 0.25544313860429496 1.8852633952600462 chr20 63025520 17450153 0.2768743994496198 1.6786941955319628 chr21 48129895 11701505 0.24312342671846676 1.9000897726805726 chr22 51304566 9477974 0.18473938557437558 1.5525959403104888 chrMT 16571 860230 51.911773580351216 42.165421395489176 chrX 155270560 22776535 0.14668933376681323 1.1689224308690414 chrY 59373566 6014803 0.10130439192417717 1.665423912839743