BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618579.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 59,448,052 number of mapped reads = 56,974,832 (95.84%) number of supplementary alignments = 133,798 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 28,715,841 number of mapped paired reads (second in pair) = 28,258,991 number of mapped paired reads (both in pair) = 55,987,386 number of mapped paired reads (singletons) = 987,446 number of mapped bases = 5,400,803,768 bp number of sequenced bases = 5,397,121,075 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,891,316 duplication rate = 19.61% >>>>>>> Insert size mean insert size = 41,293.373 std insert size = 2,013,654.5784 median insert size = 194 >>>>>>> Mapping quality mean mapping quality = 52.0553 >>>>>>> ACTG content number of A's = 1,464,516,547 bp (27.14%) number of C's = 1,193,064,583 bp (22.11%) number of T's = 1,481,090,802 bp (27.44%) number of G's = 1,258,286,084 bp (23.31%) number of N's = 163,059 bp (0%) GC percentage = 45.42% >>>>>>> Mismatches and indels general error rate = 0.0126 number of mismatches = 66,430,973 number of insertions = 954,707 mapped reads with insertion percentage = 1.65% number of deletions = 2,709,871 mapped reads with deletion percentage = 4.64% homopolymer indels = 52.96% >>>>>>> Coverage mean coverageData = 1.7446X std coverageData = 7.0759X There is a 27.68% of reference with a coverageData >= 1X There is a 19.42% of reference with a coverageData >= 2X There is a 14.76% of reference with a coverageData >= 3X There is a 11.89% of reference with a coverageData >= 4X There is a 9.83% of reference with a coverageData >= 5X There is a 8.32% of reference with a coverageData >= 6X There is a 7.15% of reference with a coverageData >= 7X There is a 6.21% of reference with a coverageData >= 8X There is a 5.45% of reference with a coverageData >= 9X There is a 4.82% of reference with a coverageData >= 10X There is a 4.29% of reference with a coverageData >= 11X There is a 3.85% of reference with a coverageData >= 12X There is a 3.46% of reference with a coverageData >= 13X There is a 3.13% of reference with a coverageData >= 14X There is a 2.84% of reference with a coverageData >= 15X There is a 2.59% of reference with a coverageData >= 16X There is a 2.36% of reference with a coverageData >= 17X There is a 2.17% of reference with a coverageData >= 18X There is a 1.99% of reference with a coverageData >= 19X There is a 1.83% of reference with a coverageData >= 20X There is a 1.69% of reference with a coverageData >= 21X There is a 1.56% of reference with a coverageData >= 22X There is a 1.45% of reference with a coverageData >= 23X There is a 1.35% of reference with a coverageData >= 24X There is a 1.25% of reference with a coverageData >= 25X There is a 1.17% of reference with a coverageData >= 26X There is a 1.09% of reference with a coverageData >= 27X There is a 1.02% of reference with a coverageData >= 28X There is a 0.95% of reference with a coverageData >= 29X There is a 0.89% of reference with a coverageData >= 30X There is a 0.83% of reference with a coverageData >= 31X There is a 0.78% of reference with a coverageData >= 32X There is a 0.74% of reference with a coverageData >= 33X There is a 0.69% of reference with a coverageData >= 34X There is a 0.65% of reference with a coverageData >= 35X There is a 0.61% of reference with a coverageData >= 36X There is a 0.58% of reference with a coverageData >= 37X There is a 0.55% of reference with a coverageData >= 38X There is a 0.52% of reference with a coverageData >= 39X There is a 0.49% of reference with a coverageData >= 40X There is a 0.46% of reference with a coverageData >= 41X There is a 0.44% of reference with a coverageData >= 42X There is a 0.41% of reference with a coverageData >= 43X There is a 0.39% of reference with a coverageData >= 44X There is a 0.37% of reference with a coverageData >= 45X There is a 0.35% of reference with a coverageData >= 46X There is a 0.33% of reference with a coverageData >= 47X There is a 0.32% of reference with a coverageData >= 48X There is a 0.3% of reference with a coverageData >= 49X There is a 0.29% of reference with a coverageData >= 50X There is a 0.27% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 488059595 1.9581078395788631 8.667495282894928 chr2 243199373 465507856 1.9140997374199644 7.492923444555135 chr3 198022430 361575832 1.825933718720652 5.935857233493135 chr4 191154276 287956628 1.50640955580821 5.897219590224871 chr5 180915260 325590335 1.7996842002161675 5.7718927715998785 chr6 171115067 304347747 1.7786145447963386 6.682446595946946 chr7 159138663 277244142 1.7421545259557698 6.001100612365754 chr8 146364022 279148429 1.9072202661935596 6.270768235046259 chr9 141213431 247282195 1.7511237652741403 8.683611001422424 chr10 135534747 280978689 2.073111841939691 6.865499702652837 chr11 135006516 283449469 2.0995243592538895 9.013876687906352 chr12 133851895 248509623 1.8566014549140302 6.186794215737308 chr13 115169878 151451352 1.3150257222639412 4.869457068771855 chr14 107349540 175135453 1.6314504281993196 5.978790620361365 chr15 102531392 186762692 1.8215171798311292 7.220181201039091 chr16 90354753 197235447 2.1829006272641793 9.945997148838272 chr17 81195210 181824924 2.23935530187064 7.874203303452748 chr18 78077248 144048412 1.8449473526525935 8.716757021720847 chr19 59128983 121536702 2.0554505731985953 8.283937768826268 chr20 63025520 158395041 2.513188959012159 7.985778450388026 chr21 48129895 70957903 1.4742999750986368 9.819073533256132 chr22 51304566 102814111 2.0039953363994933 8.038660589435937 chrMT 16571 9854 0.5946533099993966 2.9976661361095056 chrX 155270560 9140145 0.05886592410048627 1.9008997708207536 chrY 59373566 51841192 0.8731359002422054 5.239181409216119