BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617396.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 28,725,495 (89.77%) number of supplementary alignments = 396,188 (1.24%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,582,246 number of mapped paired reads (second in pair) = 14,143,249 number of mapped paired reads (both in pair) = 27,965,620 number of mapped paired reads (singletons) = 759,875 number of mapped bases = 2,803,173,976 bp number of sequenced bases = 2,802,567,455 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,242,825 duplication rate = 3.96% >>>>>>> Insert size mean insert size = 49,640.2212 std insert size = 2,127,999.4289 median insert size = 208 >>>>>>> Mapping quality mean mapping quality = 53.7379 >>>>>>> ACTG content number of A's = 836,390,501 bp (29.84%) number of C's = 562,862,434 bp (20.08%) number of T's = 827,251,353 bp (29.52%) number of G's = 574,193,913 bp (20.49%) number of N's = 1,869,254 bp (0.07%) GC percentage = 40.57% >>>>>>> Mismatches and indels general error rate = 0.0158 number of mismatches = 43,860,704 number of insertions = 229,364 mapped reads with insertion percentage = 0.79% number of deletions = 277,505 mapped reads with deletion percentage = 0.95% homopolymer indels = 43.72% >>>>>>> Coverage mean coverageData = 0.9055X std coverageData = 2.767X There is a 28.95% of reference with a coverageData >= 1X There is a 16.38% of reference with a coverageData >= 2X There is a 10.37% of reference with a coverageData >= 3X There is a 7.11% of reference with a coverageData >= 4X There is a 5.13% of reference with a coverageData >= 5X There is a 3.84% of reference with a coverageData >= 6X There is a 2.95% of reference with a coverageData >= 7X There is a 2.32% of reference with a coverageData >= 8X There is a 1.86% of reference with a coverageData >= 9X There is a 1.52% of reference with a coverageData >= 10X There is a 1.25% of reference with a coverageData >= 11X There is a 1.04% of reference with a coverageData >= 12X There is a 0.88% of reference with a coverageData >= 13X There is a 0.75% of reference with a coverageData >= 14X There is a 0.64% of reference with a coverageData >= 15X There is a 0.55% of reference with a coverageData >= 16X There is a 0.48% of reference with a coverageData >= 17X There is a 0.42% of reference with a coverageData >= 18X There is a 0.37% of reference with a coverageData >= 19X There is a 0.32% of reference with a coverageData >= 20X There is a 0.29% of reference with a coverageData >= 21X There is a 0.25% of reference with a coverageData >= 22X There is a 0.23% of reference with a coverageData >= 23X There is a 0.2% of reference with a coverageData >= 24X There is a 0.18% of reference with a coverageData >= 25X There is a 0.16% of reference with a coverageData >= 26X There is a 0.15% of reference with a coverageData >= 27X There is a 0.13% of reference with a coverageData >= 28X There is a 0.12% of reference with a coverageData >= 29X There is a 0.11% of reference with a coverageData >= 30X There is a 0.1% of reference with a coverageData >= 31X There is a 0.09% of reference with a coverageData >= 32X There is a 0.08% of reference with a coverageData >= 33X There is a 0.08% of reference with a coverageData >= 34X There is a 0.07% of reference with a coverageData >= 35X There is a 0.07% of reference with a coverageData >= 36X There is a 0.06% of reference with a coverageData >= 37X There is a 0.06% of reference with a coverageData >= 38X There is a 0.05% of reference with a coverageData >= 39X There is a 0.05% of reference with a coverageData >= 40X There is a 0.04% of reference with a coverageData >= 41X There is a 0.04% of reference with a coverageData >= 42X There is a 0.04% of reference with a coverageData >= 43X There is a 0.04% of reference with a coverageData >= 44X There is a 0.03% of reference with a coverageData >= 45X There is a 0.03% of reference with a coverageData >= 46X There is a 0.03% of reference with a coverageData >= 47X There is a 0.03% of reference with a coverageData >= 48X There is a 0.03% of reference with a coverageData >= 49X There is a 0.02% of reference with a coverageData >= 50X There is a 0.02% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 180375505 0.7236712361089764 2.5885756969984848 chr2 243199373 279969517 1.1511934161113153 2.9138594711890424 chr3 198022430 237214744 1.197918559023844 3.238528316478115 chr4 191154276 135462158 0.7086535589713934 2.1644316203714453 chr5 180915260 179708655 0.9933305515521466 2.736403171150019 chr6 171115067 128764184 0.7525005615081225 2.4618973037882816 chr7 159138663 209937750 1.3192127295929337 3.0700941727852378 chr8 146364022 124036137 0.8474496348563036 3.0684641998107276 chr9 141213431 112160264 0.7942605969257981 2.462526315633042 chr10 135534747 89781644 0.6624252893614063 2.2735292068550397 chr11 135006516 207307275 1.5355353292725515 3.627579900893881 chr12 133851895 133744778 0.9991997349010262 2.638755316057943 chr13 115169878 122110940 1.060268032931319 2.6352094055948863 chr14 107349540 81395860 0.7582320334116011 2.7419370759644885 chr15 102531392 64093682 0.6251127654640639 2.223576777369194 chr16 90354753 70107498 0.7759137806508087 3.1143768314498326 chr17 81195210 85917898 1.0581646134051503 3.493239509841743 chr18 78077248 40337741 0.5166388677018944 1.8916027057012763 chr19 59128983 39651642 0.6705957043096784 2.194456880250338 chr20 63025520 94849495 1.5049379203852662 4.447259325433278 chr21 48129895 38374918 0.7973197946930904 2.397743919051039 chr22 51304566 22303019 0.43471801320763537 1.946241469581153 chrMT 16571 165733 10.00138796693018 5.063527365981329 chrX 155270560 123167749 0.7932459894522181 2.4346290471765446 chrY 59373566 2235190 0.03764621447867895 0.5180008243260945