BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089608.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 11,247,529 number of mapped reads = 9,363,468 (83.25%) number of supplementary alignments = 359 (0%) number of secondary alignments = 0 number of mapped bases = 440,342,420 bp number of sequenced bases = 440,258,093 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,523,427 duplication rate = 29.38% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0698 >>>>>>> ACTG content number of A's = 140,574,030 bp (31.93%) number of C's = 86,559,139 bp (19.66%) number of T's = 111,227,123 bp (25.26%) number of G's = 101,889,148 bp (23.14%) number of N's = 8,653 bp (0%) GC percentage = 42.8% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 2,099,543 number of insertions = 17,753 mapped reads with insertion percentage = 0.19% number of deletions = 54,868 mapped reads with deletion percentage = 0.58% homopolymer indels = 44.22% >>>>>>> Coverage mean coverageData = 0.1422X std coverageData = 1.2476X There is a 4.25% of reference with a coverageData >= 1X There is a 2.2% of reference with a coverageData >= 2X There is a 1.49% of reference with a coverageData >= 3X There is a 1.11% of reference with a coverageData >= 4X There is a 0.85% of reference with a coverageData >= 5X There is a 0.68% of reference with a coverageData >= 6X There is a 0.54% of reference with a coverageData >= 7X There is a 0.44% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.25% of reference with a coverageData >= 11X There is a 0.21% of reference with a coverageData >= 12X There is a 0.18% of reference with a coverageData >= 13X There is a 0.15% of reference with a coverageData >= 14X There is a 0.13% of reference with a coverageData >= 15X There is a 0.11% of reference with a coverageData >= 16X There is a 0.1% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.07% of reference with a coverageData >= 19X There is a 0.06% 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 0.04% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.02% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% 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 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% 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 34754506 0.13943598559780518 1.3051892569315535 chr2 243199373 37281271 0.15329509504944325 1.3281177663958637 chr3 198022430 29369977 0.14831641546869212 1.213808686480027 chr4 191154276 28260230 0.14783990497811308 1.268810832675932 chr5 180915260 27329092 0.15106018143522001 1.2171743676367615 chr6 171115067 26015536 0.15203533187407747 1.2862341079025967 chr7 159138663 24535234 0.15417519248606482 1.356237585760188 chr8 146364022 22779153 0.15563355453569047 1.478444934064244 chr9 141213431 18540799 0.13129628583275482 1.1960138628085326 chr10 135534747 19602964 0.1446342316926301 1.2669015327447901 chr11 135006516 20086248 0.14877984111522438 1.3087508495132207 chr12 133851895 19762501 0.14764453652299805 1.2083280798021805 chr13 115169878 14054628 0.12203388806229351 1.0995908820161362 chr14 107349540 13572328 0.12643117054809921 1.1836101559791805 chr15 102531392 12029900 0.1173289444856069 1.0635621778277382 chr16 90354753 12674949 0.1402798256777925 1.1724969075545848 chr17 81195210 11532713 0.14203686399727275 1.1373981194917924 chr18 78077248 11552715 0.1479651921133286 1.2761861616716894 chr19 59128983 8728711 0.14762153105187012 1.2496061365696223 chr20 63025520 9295520 0.14748819208473013 1.2109219831972606 chr21 48129895 5629336 0.11696131894740265 1.139484750218834 chr22 51304566 5307032 0.10344170926229061 0.9647241239304746 chrMT 16571 47034 2.838332025828254 8.189387812736781 chrX 155270560 26369395 0.1698286848453435 1.352164560630481 chrY 59373566 1230648 0.020727203752592526 0.4446462688723853