BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174034.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 = 3,876,646 number of mapped reads = 3,763,868 (97.09%) number of supplementary alignments = 377,713 (9.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 1,888,008 number of mapped paired reads (second in pair) = 1,875,860 number of mapped paired reads (both in pair) = 3,687,138 number of mapped paired reads (singletons) = 76,730 number of mapped bases = 444,096,100 bp number of sequenced bases = 443,858,252 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,874,686 duplication rate = 63.74% >>>>>>> Insert size mean insert size = 876,602.2227 std insert size = 8,483,539.4907 median insert size = 203 >>>>>>> Mapping quality mean mapping quality = 52.5984 >>>>>>> ACTG content number of A's = 133,714,672 bp (30.13%) number of C's = 86,766,695 bp (19.55%) number of T's = 133,493,216 bp (30.08%) number of G's = 89,878,558 bp (20.25%) number of N's = 5,111 bp (0%) GC percentage = 39.8% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 4,655,336 number of insertions = 46,258 mapped reads with insertion percentage = 1.18% number of deletions = 96,010 mapped reads with deletion percentage = 2.49% homopolymer indels = 43.63% >>>>>>> Coverage mean coverageData = 0.1435X std coverageData = 2.1886X There is a 3.14% of reference with a coverageData >= 1X There is a 2.45% of reference with a coverageData >= 2X There is a 1.87% of reference with a coverageData >= 3X There is a 1.51% of reference with a coverageData >= 4X There is a 1.13% of reference with a coverageData >= 5X There is a 0.9% of reference with a coverageData >= 6X There is a 0.66% of reference with a coverageData >= 7X There is a 0.53% of reference with a coverageData >= 8X There is a 0.38% of reference with a coverageData >= 9X There is a 0.32% 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 0.12% 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 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% 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 32181257 0.12911204341593194 1.3085387147071086 chr2 243199373 38557927 0.1585445164778447 6.340687460332727 chr3 198022430 34715676 0.17531183714895326 1.1829256701294557 chr4 191154276 35712739 0.18682678592028984 1.4461735417591566 chr5 180915260 18709699 0.10341692016472243 0.9020639075220199 chr6 171115067 21634191 0.1264306608371313 1.0285568639067564 chr7 159138663 34154333 0.2146199569365491 2.0426573534281056 chr8 146364022 28072386 0.19179840521190378 1.5152209043165197 chr9 141213431 16223009 0.11488290373739309 1.1342780825309777 chr10 135534747 18044191 0.1331333211549065 2.298523645892312 chr11 135006516 13589389 0.10065728234924602 0.9081433520830042 chr12 133851895 23274015 0.17387886066162903 1.1810953493248766 chr13 115169878 5168746 0.04487932165735211 0.6011343243601401 chr14 107349540 19174300 0.17861557674117653 1.1973615274089162 chr15 102531392 11069875 0.10796571453940662 0.9138980469597201 chr16 90354753 14023499 0.15520488446246983 1.5890919797124121 chr17 81195210 13891717 0.1710903512657951 1.2030143599578809 chr18 78077248 3899967 0.04995010838496767 1.218322498782784 chr19 59128983 9274523 0.15685240180775645 1.3082445619774963 chr20 63025520 17927956 0.2844555031041394 1.5251009913133273 chr21 48129895 5692280 0.11826911319877179 1.0072550474085091 chr22 51304566 3689503 0.07191373570921543 0.722909708330898 chrMT 16571 1199133 72.36334560376561 54.552136393423794 chrX 155270560 23302264 0.15007522353239403 1.1047940761721224 chrY 59373566 913525 0.015386055808067853 0.6447852265636976