BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173959.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 = 14,216,420 number of mapped reads = 13,876,111 (97.61%) number of supplementary alignments = 1,833,627 (12.9%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,940,727 number of mapped paired reads (second in pair) = 6,935,384 number of mapped paired reads (both in pair) = 13,654,616 number of mapped paired reads (singletons) = 221,495 number of mapped bases = 1,581,518,412 bp number of sequenced bases = 1,580,475,910 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,483,568 duplication rate = 67.01% >>>>>>> Insert size mean insert size = 957,402.1879 std insert size = 9,269,464.0759 median insert size = 161 >>>>>>> Mapping quality mean mapping quality = 52.443 >>>>>>> ACTG content number of A's = 471,513,723 bp (29.83%) number of C's = 314,522,547 bp (19.9%) number of T's = 467,136,732 bp (29.56%) number of G's = 327,291,076 bp (20.71%) number of N's = 11,832 bp (0%) GC percentage = 40.61% >>>>>>> Mismatches and indels general error rate = 0.009 number of mismatches = 13,748,438 number of insertions = 178,628 mapped reads with insertion percentage = 1.23% number of deletions = 436,028 mapped reads with deletion percentage = 3.06% homopolymer indels = 41.35% >>>>>>> Coverage mean coverageData = 0.5109X std coverageData = 8.4869X There is a 9.71% of reference with a coverageData >= 1X There is a 7.63% of reference with a coverageData >= 2X There is a 5.97% of reference with a coverageData >= 3X There is a 4.9% of reference with a coverageData >= 4X There is a 3.81% of reference with a coverageData >= 5X There is a 3.15% of reference with a coverageData >= 6X There is a 2.43% of reference with a coverageData >= 7X There is a 2.07% of reference with a coverageData >= 8X There is a 1.61% of reference with a coverageData >= 9X There is a 1.42% of reference with a coverageData >= 10X There is a 1.1% of reference with a coverageData >= 11X There is a 0.99% of reference with a coverageData >= 12X There is a 0.76% of reference with a coverageData >= 13X There is a 0.7% of reference with a coverageData >= 14X There is a 0.54% of reference with a coverageData >= 15X There is a 0.49% of reference with a coverageData >= 16X There is a 0.38% of reference with a coverageData >= 17X There is a 0.35% of reference with a coverageData >= 18X There is a 0.27% of reference with a coverageData >= 19X There is a 0.25% of reference with a coverageData >= 20X There is a 0.19% of reference with a coverageData >= 21X There is a 0.18% of reference with a coverageData >= 22X There is a 0.14% of reference with a coverageData >= 23X There is a 0.13% of reference with a coverageData >= 24X There is a 0.1% of reference with a coverageData >= 25X There is a 0.1% of reference with a coverageData >= 26X There is a 0.08% of reference with a coverageData >= 27X There is a 0.07% of reference with a coverageData >= 28X There is a 0.06% of reference with a coverageData >= 29X There is a 0.05% of reference with a coverageData >= 30X There is a 0.04% of reference with a coverageData >= 31X There is a 0.04% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% 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 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 126255123 0.506538850308421 4.168379869181978 chr2 243199373 141965793 0.5837424301254264 27.736539261452446 chr3 198022430 109116000 0.5510284870254344 2.3406695539472464 chr4 191154276 105753002 0.5532337764706869 4.150979708081496 chr5 180915260 95513254 0.5279447073729435 2.2760650583520086 chr6 171115067 94729240 0.5535996429817603 3.2720510893320567 chr7 159138663 89269663 0.560955215515415 4.165316986852451 chr8 146364022 81925434 0.5597375152754411 5.252374629639893 chr9 141213431 67179683 0.47573154001194123 3.9980199435662183 chr10 135534747 77765860 0.5737706508575251 5.466295363042877 chr11 135006516 70975166 0.5257165957826806 2.461002706419237 chr12 133851895 72342377 0.5404658409953778 2.5012692728390773 chr13 115169878 51712897 0.4490140816160281 2.099746062571268 chr14 107349540 49062932 0.457039052053693 2.2118452098441352 chr15 102531392 45405912 0.4428488789072521 2.2242969812560336 chr16 90354753 47820249 0.5292499554506004 3.38929931558534 chr17 81195210 44098499 0.5431170016063755 2.8190726154334156 chr18 78077248 43740027 0.5602147632047687 5.5125537623729794 chr19 59128983 30775327 0.5204778678503569 3.390956089830906 chr20 63025520 34893773 0.5536451424756194 2.6334588669182697 chr21 48129895 22932828 0.4764778315016062 3.631473358264007 chr22 51304566 19865908 0.38721520419839434 2.737912328151222 chrMT 16571 2924427 176.47860720535877 135.6341028806334 chrX 155270560 42888103 0.2762152915530156 1.6994765955736764 chrY 59373566 12606935 0.21233245447982693 3.2238731006413768