BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173869.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 = 3,529,804 number of mapped reads = 3,442,828 (97.54%) number of supplementary alignments = 343,564 (9.73%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,724,461 number of mapped paired reads (second in pair) = 1,718,367 number of mapped paired reads (both in pair) = 3,385,942 number of mapped paired reads (singletons) = 56,886 number of mapped bases = 405,357,865 bp number of sequenced bases = 405,121,834 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,642,661 duplication rate = 63.69% >>>>>>> Insert size mean insert size = 844,566.7442 std insert size = 8,826,288.745 median insert size = 195 >>>>>>> Mapping quality mean mapping quality = 52.7094 >>>>>>> ACTG content number of A's = 121,172,865 bp (29.91%) number of C's = 80,387,594 bp (19.84%) number of T's = 120,634,275 bp (29.78%) number of G's = 82,922,268 bp (20.47%) number of N's = 4,832 bp (0%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0105 number of mismatches = 4,151,040 number of insertions = 41,938 mapped reads with insertion percentage = 1.18% number of deletions = 94,382 mapped reads with deletion percentage = 2.67% homopolymer indels = 43.28% >>>>>>> Coverage mean coverageData = 0.1309X std coverageData = 1.988X There is a 2.82% of reference with a coverageData >= 1X There is a 2.18% of reference with a coverageData >= 2X There is a 1.66% of reference with a coverageData >= 3X There is a 1.36% of reference with a coverageData >= 4X There is a 1.02% of reference with a coverageData >= 5X There is a 0.83% of reference with a coverageData >= 6X There is a 0.61% of reference with a coverageData >= 7X There is a 0.5% of reference with a coverageData >= 8X There is a 0.37% of reference with a coverageData >= 9X There is a 0.31% of reference with a coverageData >= 10X There is a 0.23% of reference with a coverageData >= 11X There is a 0.2% of reference with a coverageData >= 12X There is a 0.14% of reference with a coverageData >= 13X There is a 0.13% of reference with a coverageData >= 14X There is a 0.09% of reference with a coverageData >= 15X There is a 0.08% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% 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% 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 39802414 0.1596883243071238 1.5182589830588085 chr2 243199373 39907685 0.16409452256276993 5.689431857948604 chr3 198022430 30668781 0.15487528862260705 1.1500081648652203 chr4 191154276 22121565 0.11572623674921088 1.1122157988387888 chr5 180915260 24963644 0.13798528659218687 1.0850925663188147 chr6 171115067 20052003 0.11718432135493947 1.0082179568645864 chr7 159138663 25202207 0.1583663361555325 1.6127954391905803 chr8 146364022 16005664 0.10935518019585441 1.0597202036320827 chr9 141213431 17523140 0.12408975460698211 1.1273279819854836 chr10 135534747 16185706 0.11942108100146452 1.8359053011758704 chr11 135006516 20043095 0.14846020469115728 1.1262482383990535 chr12 133851895 14086953 0.10524283574767469 0.9370848300693945 chr13 115169878 12500193 0.1085369995790045 0.9705527111321298 chr14 107349540 9474117 0.08825484487404417 0.8581169242313701 chr15 102531392 13996692 0.13651128427086995 1.056861503343856 chr16 90354753 18221337 0.2016643994367402 1.6672110397072748 chr17 81195210 11452076 0.14104373891021404 1.0941052408703593 chr18 78077248 5505228 0.07051001592679086 1.2439797208502081 chr19 59128983 9370587 0.15847705346124422 1.480702133724417 chr20 63025520 13491564 0.2140650961705671 1.3363427659837372 chr21 48129895 6006711 0.12480207987156423 1.058918079207861 chr22 51304566 4622606 0.0901012592134587 0.8153027687361853 chrMT 16571 1368358 82.57546315852996 65.7553576740277 chrX 155270560 12256816 0.07893844138901798 0.7977218319150087 chrY 59373566 528723 0.008905023491430512 0.42378601869201504