BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174039.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 = 2,885,004 number of mapped reads = 2,819,452 (97.73%) number of supplementary alignments = 286,617 (9.93%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,410,122 number of mapped paired reads (second in pair) = 1,409,330 number of mapped paired reads (both in pair) = 2,777,380 number of mapped paired reads (singletons) = 42,072 number of mapped bases = 332,693,007 bp number of sequenced bases = 332,492,133 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,083,807 duplication rate = 62.66% >>>>>>> Insert size mean insert size = 825,297.2291 std insert size = 8,389,364.4176 median insert size = 192 >>>>>>> Mapping quality mean mapping quality = 52.7074 >>>>>>> ACTG content number of A's = 100,904,582 bp (30.35%) number of C's = 64,463,433 bp (19.39%) number of T's = 100,589,348 bp (30.25%) number of G's = 66,530,498 bp (20.01%) number of N's = 4,272 bp (0%) GC percentage = 39.4% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 3,383,070 number of insertions = 35,125 mapped reads with insertion percentage = 1.2% number of deletions = 80,098 mapped reads with deletion percentage = 2.77% homopolymer indels = 42.72% >>>>>>> Coverage mean coverageData = 0.1075X std coverageData = 1.7105X There is a 2.57% of reference with a coverageData >= 1X There is a 1.94% of reference with a coverageData >= 2X There is a 1.41% of reference with a coverageData >= 3X There is a 1.12% of reference with a coverageData >= 4X There is a 0.8% of reference with a coverageData >= 5X There is a 0.64% of reference with a coverageData >= 6X There is a 0.45% of reference with a coverageData >= 7X There is a 0.37% of reference with a coverageData >= 8X There is a 0.26% of reference with a coverageData >= 9X There is a 0.22% of reference with a coverageData >= 10X There is a 0.15% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% 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 29587025 0.11870391689014087 1.435285105369628 chr2 243199373 35271547 0.14503140598146197 4.766019227563384 chr3 198022430 24330101 0.12286537944211673 0.9597248761784511 chr4 191154276 20165305 0.10549230402776864 1.0010013371663116 chr5 180915260 23686924 0.13092828100846773 0.994859249313842 chr6 171115067 18522756 0.1082473701745972 0.9163202569387736 chr7 159138663 21053449 0.13229625411644938 1.5961250734938437 chr8 146364022 15020285 0.10262279482863623 0.985908056298441 chr9 141213431 13801479 0.0977348889710073 0.9904269355114512 chr10 135534747 13441019 0.09917028140392663 1.7083614335779147 chr11 135006516 15667653 0.11605108748973272 0.9414890177251845 chr12 133851895 12079338 0.09024405668668344 0.8213139098895939 chr13 115169878 10889993 0.09455591330920747 0.8492682136078606 chr14 107349540 8043856 0.07493144358140706 0.7485433681707093 chr15 102531392 10744617 0.10479343731137485 0.8681180227851392 chr16 90354753 13546798 0.14992900262811854 1.4505821418904201 chr17 81195210 7372042 0.09079405053573973 0.8945755220257247 chr18 78077248 5210351 0.06673328189026334 1.1368470120135712 chr19 59128983 6224194 0.10526468889207853 1.5425716183437486 chr20 63025520 9588268 0.15213310417748238 1.042521444186156 chr21 48129895 3701162 0.07689944056599333 0.7784094321849376 chr22 51304566 2828323 0.055128095226456064 0.6066836350253711 chrMT 16571 1037265 62.59519642749382 53.62457730806118 chrX 155270560 10416873 0.06708852598973045 0.6980163574747512 chrY 59373566 462384 0.0077877080854466445 0.35489865021142125