BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617664.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 = 30,512,494 (95.35%) number of supplementary alignments = 144,215 (0.45%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,327,514 number of mapped paired reads (second in pair) = 15,184,980 number of mapped paired reads (both in pair) = 29,948,862 number of mapped paired reads (singletons) = 563,632 number of mapped bases = 2,966,255,689 bp number of sequenced bases = 2,964,445,895 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,050,574 duplication rate = 10.78% >>>>>>> Insert size mean insert size = 31,799.3064 std insert size = 1,635,581.4303 median insert size = 224 >>>>>>> Mapping quality mean mapping quality = 52.7071 >>>>>>> ACTG content number of A's = 882,343,183 bp (29.76%) number of C's = 591,417,955 bp (19.95%) number of T's = 881,090,042 bp (29.72%) number of G's = 607,879,079 bp (20.51%) number of N's = 1,715,636 bp (0.06%) GC percentage = 40.46% >>>>>>> Mismatches and indels general error rate = 0.0146 number of mismatches = 42,363,616 number of insertions = 463,184 mapped reads with insertion percentage = 1.49% number of deletions = 1,090,864 mapped reads with deletion percentage = 3.5% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.9582X std coverageData = 10.7546X There is a 33.44% of reference with a coverageData >= 1X There is a 19.44% of reference with a coverageData >= 2X There is a 11.92% of reference with a coverageData >= 3X There is a 7.64% of reference with a coverageData >= 4X There is a 5.04% of reference with a coverageData >= 5X There is a 3.42% of reference with a coverageData >= 6X There is a 2.38% of reference with a coverageData >= 7X There is a 1.69% of reference with a coverageData >= 8X There is a 1.23% of reference with a coverageData >= 9X There is a 0.91% of reference with a coverageData >= 10X There is a 0.68% of reference with a coverageData >= 11X There is a 0.52% of reference with a coverageData >= 12X There is a 0.41% of reference with a coverageData >= 13X There is a 0.32% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.21% of reference with a coverageData >= 16X There is a 0.17% of reference with a coverageData >= 17X There is a 0.14% of reference with a coverageData >= 18X There is a 0.12% of reference with a coverageData >= 19X There is a 0.1% of reference with a coverageData >= 20X There is a 0.09% of reference with a coverageData >= 21X There is a 0.08% of reference with a coverageData >= 22X There is a 0.07% of reference with a coverageData >= 23X There is a 0.06% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.04% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.03% of reference with a coverageData >= 33X There is a 0.03% of reference with a coverageData >= 34X There is a 0.03% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.02% of reference with a coverageData >= 48X There is a 0.02% 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 182061915 0.7304371570652978 10.38446473782832 chr2 243199373 306746362 1.2612958586862804 12.338754897584048 chr3 198022430 248670856 1.255771156833092 2.5014633591406326 chr4 191154276 165822310 0.8674789466912056 8.508992055940789 chr5 180915260 196352090 1.0853263013855217 2.3491395414383356 chr6 171115067 143590202 0.8391441181506243 5.8962610631282635 chr7 159138663 231907305 1.4572656363212 13.440283130794032 chr8 146364022 132024766 0.9020301860794725 4.151389952071836 chr9 141213431 121759723 0.8622389679066718 20.992872193071985 chr10 135534747 125581621 0.9265640271568146 21.852807291570418 chr11 135006516 162920340 1.2067590870947296 12.176127207055565 chr12 133851895 126601592 0.9458333929452399 2.1613746391701016 chr13 115169878 127334811 1.105625995366601 2.3029080377270073 chr14 107349540 84877245 0.7906624006027413 2.5051478864089396 chr15 102531392 63255503 0.6169379130247251 1.5810352468972326 chr16 90354753 82060037 0.9081983434784001 16.967509017490286 chr17 81195210 73231382 0.9019175145923017 12.737543498671199 chr18 78077248 54861178 0.7026525576311297 18.401514061183807 chr19 59128983 31611455 0.5346186150368931 6.293762951186049 chr20 63025520 80291168 1.2739469345116075 3.070342470574045 chr21 48129895 43165225 0.8968485179533427 4.419507917091215 chr22 51304566 19075511 0.3718092264926284 1.283411589396626 chrMT 16571 3151973 190.21018647033975 131.03975033407116 chrX 155270560 147451240 0.9496406788254 4.3188767697573205 chrY 59373566 11849879 0.19958172968758522 17.485999913513385