BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926990.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 29,719,630 number of mapped reads = 29,235,255 (98.37%) number of supplementary alignments = 626,757 (2.11%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,681,327 number of mapped paired reads (second in pair) = 14,553,928 number of mapped paired reads (both in pair) = 28,980,352 number of mapped paired reads (singletons) = 254,903 number of mapped bases = 2,735,161,038 bp number of sequenced bases = 2,733,043,267 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,479,211 duplication rate = 6.48% >>>>>>> Insert size mean insert size = 206,577.5679 std insert size = 4,483,611.1992 median insert size = 171 >>>>>>> Mapping quality mean mapping quality = 53.2067 >>>>>>> ACTG content number of A's = 771,471,918 bp (28.23%) number of C's = 556,037,368 bp (20.34%) number of T's = 780,331,800 bp (28.55%) number of G's = 625,008,565 bp (22.87%) number of N's = 193,616 bp (0.01%) GC percentage = 43.21% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 25,994,628 number of insertions = 468,295 mapped reads with insertion percentage = 1.57% number of deletions = 1,458,097 mapped reads with deletion percentage = 4.86% homopolymer indels = 52.14% >>>>>>> Coverage mean coverageData = 0.8835X std coverageData = 3.5645X There is a 32.49% of reference with a coverageData >= 1X There is a 19.02% of reference with a coverageData >= 2X There is a 11.35% of reference with a coverageData >= 3X There is a 7.26% of reference with a coverageData >= 4X There is a 4.79% of reference with a coverageData >= 5X There is a 3.25% of reference with a coverageData >= 6X There is a 2.26% of reference with a coverageData >= 7X There is a 1.6% of reference with a coverageData >= 8X There is a 1.15% of reference with a coverageData >= 9X There is a 0.84% of reference with a coverageData >= 10X There is a 0.63% of reference with a coverageData >= 11X There is a 0.47% of reference with a coverageData >= 12X There is a 0.36% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.22% of reference with a coverageData >= 15X There is a 0.17% of reference with a coverageData >= 16X There is a 0.14% of reference with a coverageData >= 17X There is a 0.11% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.07% 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 0.03% 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 0.02% 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 0.01% 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 0.01% 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 237748303 0.9538523998301293 3.7994688386336133 chr2 243199373 242568533 0.9974060788388628 5.627126524076891 chr3 198022430 181808538 0.9181209320580502 1.9343797301303483 chr4 191154276 146216136 0.7649116674742866 2.731763064682831 chr5 180915260 150366737 0.8311445756427622 1.8085691570527853 chr6 171115067 140509708 0.8211416473337207 2.725785909773757 chr7 159138663 143334535 0.9006895766115617 2.751554909536833 chr8 146364022 132110416 0.9026153708730414 2.3386253743159275 chr9 141213431 114702797 0.8122654919417687 4.293098757785547 chr10 135534747 136228841 1.00512115169994 4.253949695015447 chr11 135006516 133460288 0.9885470120568106 3.134284183674504 chr12 133851895 114187034 0.8530849264405259 2.034310876801402 chr13 115169878 78729916 0.6835981540242666 1.6684824979774444 chr14 107349540 80627094 0.751070698579612 1.86501995341621 chr15 102531392 89481316 0.872721166216099 2.073149702734235 chr16 90354753 99639479 1.1027585787324325 5.339389246858443 chr17 81195210 87115044 1.072908660498569 3.3559626678689014 chr18 78077248 64229988 0.822646669103911 4.449614792995128 chr19 59128983 58192041 0.9841542683052743 2.8147599869632316 chr20 63025520 72632723 1.1524335380334823 2.442433716501096 chr21 48129895 32195903 0.6689377360993619 3.443111783406622 chr22 51304566 44001161 0.8576461011286988 2.2345545663852486 chrMT 16571 7867269 474.7612696880092 361.78583905160974 chrX 155270560 141956882 0.9142549753153463 2.19064718405985 chrY 59373566 5250356 0.08842918412547429 2.9490310281959773