BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173925.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 = 5,643,304 number of mapped reads = 5,518,147 (97.78%) number of supplementary alignments = 528,165 (9.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,763,334 number of mapped paired reads (second in pair) = 2,754,813 number of mapped paired reads (both in pair) = 5,439,186 number of mapped paired reads (singletons) = 78,961 number of mapped bases = 656,744,895 bp number of sequenced bases = 656,375,597 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,492,533 duplication rate = 67.02% >>>>>>> Insert size mean insert size = 918,933.5888 std insert size = 8,910,298.3396 median insert size = 204 >>>>>>> Mapping quality mean mapping quality = 52.9858 >>>>>>> ACTG content number of A's = 194,709,120 bp (29.66%) number of C's = 131,575,906 bp (20.05%) number of T's = 194,338,955 bp (29.61%) number of G's = 135,743,604 bp (20.68%) number of N's = 8,012 bp (0%) GC percentage = 40.73% >>>>>>> Mismatches and indels general error rate = 0.0101 number of mismatches = 6,508,709 number of insertions = 64,093 mapped reads with insertion percentage = 1.13% number of deletions = 155,391 mapped reads with deletion percentage = 2.76% homopolymer indels = 43.66% >>>>>>> Coverage mean coverageData = 0.2121X std coverageData = 2.8755X There is a 3.8% of reference with a coverageData >= 1X There is a 3.11% of reference with a coverageData >= 2X There is a 2.51% of reference with a coverageData >= 3X There is a 2.15% of reference with a coverageData >= 4X There is a 1.73% of reference with a coverageData >= 5X There is a 1.45% of reference with a coverageData >= 6X There is a 1.14% of reference with a coverageData >= 7X There is a 0.95% of reference with a coverageData >= 8X There is a 0.73% of reference with a coverageData >= 9X There is a 0.61% of reference with a coverageData >= 10X There is a 0.47% of reference with a coverageData >= 11X There is a 0.4% 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 0.21% of reference with a coverageData >= 15X There is a 0.19% of reference with a coverageData >= 16X There is a 0.15% of reference with a coverageData >= 17X There is a 0.13% of reference with a coverageData >= 18X There is a 0.1% of reference with a coverageData >= 19X There is a 0.09% of reference with a coverageData >= 20X There is a 0.07% 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 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% 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 0.02% 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 54247417 0.21764205353775226 1.7147730918989996 chr2 243199373 58741184 0.24153509639188092 8.737105811906435 chr3 198022430 47730428 0.24103546249785945 1.56930722531101 chr4 191154276 30143980 0.15769451058473838 1.3455336187777487 chr5 180915260 39234711 0.21686789163058992 1.4452313754892243 chr6 171115067 28606811 0.16717879670993555 1.392832801064332 chr7 159138663 33046784 0.20766030942461794 1.6219649735644877 chr8 146364022 31926070 0.21812785385195277 1.649388898327837 chr9 141213431 29289424 0.2074124521484079 1.5768326987592125 chr10 135534747 30062121 0.2218037932368738 2.05863264509047 chr11 135006516 25299354 0.18739357735888837 1.354106482247504 chr12 133851895 32106701 0.23986736235598308 1.5258948911088914 chr13 115169878 14077748 0.12223463499718216 1.093249641023574 chr14 107349540 22305086 0.20777998676100523 1.4118656685738362 chr15 102531392 23126607 0.22555635448702382 1.4795880862829436 chr16 90354753 25244303 0.27939098012918034 1.7907721696839567 chr17 81195210 34303997 0.42248793986738875 2.256608465729514 chr18 78077248 15581774 0.19956868869148667 1.784349855154 chr19 59128983 11763669 0.19894928684973323 1.5396427467493161 chr20 63025520 33578746 0.5327801500090756 2.530401463607208 chr21 48129895 8832533 0.1835144872017693 1.3535592228295001 chr22 51304566 6674008 0.13008604341375776 1.0814677043870862 chrMT 16571 276808 16.704363043871826 17.68505102413775 chrX 155270560 19649540 0.12655032608886063 1.1026875279122834 chrY 59373566 895091 0.015075580941188542 0.5560811649801641