BamQC report ----------------------------------- >>>>>>> Input bam file = SRR5038483.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 21,194,056 number of mapped reads = 18,946,362 (89.39%) number of supplementary alignments = 349,830 (1.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,636,480 number of mapped paired reads (second in pair) = 9,309,882 number of mapped paired reads (both in pair) = 18,538,464 number of mapped paired reads (singletons) = 407,898 number of mapped bases = 2,530,165,289 bp number of sequenced bases = 2,528,283,376 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,657,190 duplication rate = 13.23% >>>>>>> Insert size mean insert size = 101,204.5764 std insert size = 3,077,139.7256 median insert size = 235 >>>>>>> Mapping quality mean mapping quality = 53.3348 >>>>>>> ACTG content number of A's = 719,180,158 bp (28.45%) number of C's = 508,389,415 bp (20.11%) number of T's = 732,388,477 bp (28.97%) number of G's = 568,130,663 bp (22.47%) number of N's = 194,663 bp (0.01%) GC percentage = 42.58% >>>>>>> Mismatches and indels general error rate = 0.0142 number of mismatches = 34,386,950 number of insertions = 482,554 mapped reads with insertion percentage = 2.39% number of deletions = 911,257 mapped reads with deletion percentage = 4.62% homopolymer indels = 46.6% >>>>>>> Coverage mean coverageData = 0.8173X std coverageData = 12.0199X There is a 33.35% of reference with a coverageData >= 1X There is a 18.7% of reference with a coverageData >= 2X There is a 9.87% of reference with a coverageData >= 3X There is a 5.77% of reference with a coverageData >= 4X There is a 3.28% of reference with a coverageData >= 5X There is a 1.97% of reference with a coverageData >= 6X There is a 1.18% of reference with a coverageData >= 7X There is a 0.73% of reference with a coverageData >= 8X There is a 0.46% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.2% of reference with a coverageData >= 11X There is a 0.14% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.03% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% 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 0.02% 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 0.02% of reference with a coverageData >= 34X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 207732644 0.8334287921392982 18.29973404161188 chr2 243199373 238010204 0.9786629014047664 12.616671383628033 chr3 198022430 160663917 0.8113420131244728 1.7121855740531304 chr4 191154276 145070326 0.7589175038909409 13.513304725712425 chr5 180915260 142702010 0.7887781826696101 1.5910119498317365 chr6 171115067 149735101 0.8750550353347902 8.539832400696042 chr7 159138663 130285195 0.8186897674262853 8.788543523581211 chr8 146364022 136791599 0.9345985244925833 3.568746780119509 chr9 141213431 108185069 0.7661103354963452 17.2960855033577 chr10 135534747 142944484 1.0546703864803024 31.54583667317282 chr11 135006516 115198200 0.853278815075859 8.311848162222157 chr12 133851895 105862800 0.7908950411198885 1.7030372244386087 chr13 115169878 81861451 0.7107887272399472 1.4624009680150276 chr14 107349540 77209793 0.7192372971509705 1.6763761176865044 chr15 102531392 67722956 0.660509475966151 1.4216172692836948 chr16 90354753 89477287 0.9902886569785654 15.200661737715611 chr17 81195210 64313991 0.7920909497001116 14.986004533272975 chr18 78077248 78703285 1.008018174513528 13.65419908961736 chr19 59128983 35528873 0.6008706931421431 8.76608013214441 chr20 63025520 55264574 0.8768602623191367 4.294593866642576 chr21 48129895 29003900 0.602617146785797 6.319371313088189 chr22 51304566 19399614 0.3781264614927256 1.1585989863574677 chrMT 16571 1630710 98.40745881359001 50.23098896962856 chrX 155270560 137577861 0.8860524557907178 3.864820030149268 chrY 59373566 9289445 0.15645758922413386 13.580620560069738