BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10173846.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 = 6,680,618 number of mapped reads = 6,512,311 (97.48%) number of supplementary alignments = 681,183 (10.2%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,258,126 number of mapped paired reads (second in pair) = 3,254,185 number of mapped paired reads (both in pair) = 6,401,858 number of mapped paired reads (singletons) = 110,453 number of mapped bases = 772,873,817 bp number of sequenced bases = 772,405,674 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5,092,576 duplication rate = 64.68% >>>>>>> Insert size mean insert size = 976,525.042 std insert size = 9,089,019.8465 median insert size = 207 >>>>>>> Mapping quality mean mapping quality = 52.6733 >>>>>>> ACTG content number of A's = 230,003,112 bp (29.78%) number of C's = 153,428,385 bp (19.86%) number of T's = 229,631,351 bp (29.73%) number of G's = 159,332,525 bp (20.63%) number of N's = 10,301 bp (0%) GC percentage = 40.49% >>>>>>> Mismatches and indels general error rate = 0.0107 number of mismatches = 8,081,056 number of insertions = 78,902 mapped reads with insertion percentage = 1.17% number of deletions = 192,775 mapped reads with deletion percentage = 2.89% homopolymer indels = 42.43% >>>>>>> Coverage mean coverageData = 0.2497X std coverageData = 3.4259X There is a 5.15% of reference with a coverageData >= 1X There is a 4.07% of reference with a coverageData >= 2X There is a 3.16% of reference with a coverageData >= 3X There is a 2.6% of reference with a coverageData >= 4X There is a 2% of reference with a coverageData >= 5X There is a 1.62% of reference with a coverageData >= 6X There is a 1.21% of reference with a coverageData >= 7X There is a 0.98% of reference with a coverageData >= 8X There is a 0.73% of reference with a coverageData >= 9X There is a 0.6% of reference with a coverageData >= 10X There is a 0.45% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.25% of reference with a coverageData >= 14X There is a 0.18% of reference with a coverageData >= 15X There is a 0.16% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.05% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.04% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.02% 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 0.01% 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 0.01% 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% 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 61967975 0.2486171338365492 2.6092113806147283 chr2 243199373 67604608 0.27798019035188876 10.422326969871362 chr3 198022430 61529843 0.3107215834085058 1.643590621062507 chr4 191154276 33278399 0.17409183669006703 1.4470999505902242 chr5 180915260 45291242 0.25034506210255564 1.4428311404666914 chr6 171115067 42734686 0.2497423911828875 1.7674490807931973 chr7 159138663 42923815 0.2697258742207731 2.1365697788893856 chr8 146364022 38887477 0.2656901366102115 1.7764879964812217 chr9 141213431 31541954 0.22336369689934096 1.9100787162714485 chr10 135534747 40904005 0.3017971841567683 2.7456007335982617 chr11 135006516 29340030 0.21732306609556534 1.3942314007632575 chr12 133851895 34373085 0.25679939010202285 1.462268489432025 chr13 115169878 20031805 0.17393267534762866 1.2160743270057863 chr14 107349540 24305384 0.22641348998794034 1.368546839052234 chr15 102531392 28681004 0.279729002411281 1.5329095531906853 chr16 90354753 28166215 0.3117292014510847 1.935198215904591 chr17 81195210 33805047 0.4163428729354847 2.090413578411854 chr18 78077248 13595412 0.17412770491091079 2.813389275399685 chr19 59128983 14236972 0.24077823222496486 2.010497620201839 chr20 63025520 36139880 0.5734166096527248 2.491232329944938 chr21 48129895 9480258 0.19697233912519443 1.3228973947033744 chr22 51304566 6661489 0.12984203004465528 0.9893567186649885 chrMT 16571 1271413 76.72518254782452 59.99403481262306 chrX 155270560 25049395 0.16132739522546966 1.1602398784796215 chrY 59373566 1072424 0.01806231412814248 0.6733730241216886