BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472625.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 18,676,580 number of mapped reads = 18,532,119 (99.23%) number of supplementary alignments = 86,443 (0.46%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,285,605 number of mapped paired reads (second in pair) = 9,246,514 number of mapped paired reads (both in pair) = 18,438,708 number of mapped paired reads (singletons) = 93,411 number of mapped bases = 1,820,791,616 bp number of sequenced bases = 1,820,589,248 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,168,000 duplication rate = 50.64% >>>>>>> Insert size mean insert size = 19,839.2149 std insert size = 1,427,565.2879 median insert size = 200 >>>>>>> Mapping quality mean mapping quality = 54.7597 >>>>>>> ACTG content number of A's = 480,750,836 bp (26.41%) number of C's = 431,756,074 bp (23.72%) number of T's = 482,723,608 bp (26.51%) number of G's = 425,029,375 bp (23.35%) number of N's = 329,355 bp (0.02%) GC percentage = 47.06% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 10,611,883 number of insertions = 96,362 mapped reads with insertion percentage = 0.52% number of deletions = 86,909 mapped reads with deletion percentage = 0.46% homopolymer indels = 45.14% >>>>>>> Coverage mean coverageData = 0.5882X std coverageData = 25.9385X There is a 3.61% of reference with a coverageData >= 1X There is a 1.72% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.6% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.4% of reference with a coverageData >= 6X There is a 0.35% of reference with a coverageData >= 7X There is a 0.33% of reference with a coverageData >= 8X There is a 0.32% of reference with a coverageData >= 9X There is a 0.3% of reference with a coverageData >= 10X There is a 0.29% of reference with a coverageData >= 11X There is a 0.28% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.27% of reference with a coverageData >= 14X There is a 0.26% of reference with a coverageData >= 15X There is a 0.25% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 264675414 1.06188467229536 33.967029502711554 chr2 243199373 121091715 0.49791129601308637 22.355315151813077 chr3 198022430 133521086 0.6742725356920426 18.731822599478512 chr4 191154276 29441747 0.15402086532450887 12.902260391239068 chr5 180915260 74094978 0.4095562640763416 17.429695052846274 chr6 171115067 212473952 1.2417021816085898 45.840194942615135 chr7 159138663 94079268 0.5911779464931158 23.91562855274931 chr8 146364022 106405994 0.7269955590589059 35.13067799918394 chr9 141213431 63551144 0.450036115898919 16.12931791665887 chr10 135534747 20153393 0.1486953969080711 5.9375673783825045 chr11 135006516 43748077 0.32404418909676924 15.357609900982508 chr12 133851895 63769897 0.47642132373247315 19.90334972355642 chr13 115169878 93364290 0.810665875672804 38.3124751681304 chr14 107349540 34570404 0.3220358838985244 13.791662461826405 chr15 102531392 21861605 0.2132186501476543 13.705201385007548 chr16 90354753 89846115 0.9943706558524928 45.015629501064865 chr17 81195210 75322521 0.9276719772016108 33.63566336005719 chr18 78077248 15661432 0.20058893469196046 9.054163483335552 chr19 59128983 70830246 1.197893865348572 46.557215498842226 chr20 63025520 70161471 1.1132231991104555 31.384668807762477 chr21 48129895 9424041 0.19580431247564534 10.759603941013259 chr22 51304566 19219075 0.3746074959488011 13.095282655271797 chrMT 16571 4051 0.24446321887635025 0.6210108102340963 chrX 155270560 92886613 0.5982242416076815 20.42188262434325 chrY 59373566 633087 0.010662775417599139 0.39870925198610024