BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926891.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 = 41,774,588 number of mapped reads = 39,168,023 (93.76%) number of supplementary alignments = 444,152 (1.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 19,636,785 number of mapped paired reads (second in pair) = 19,531,238 number of mapped paired reads (both in pair) = 38,753,632 number of mapped paired reads (singletons) = 414,391 number of mapped bases = 3,721,980,720 bp number of sequenced bases = 3,719,149,301 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,263,726 duplication rate = 6.64% >>>>>>> Insert size mean insert size = 98,570.4403 std insert size = 3,107,590.2761 median insert size = 170 >>>>>>> Mapping quality mean mapping quality = 53.4036 >>>>>>> ACTG content number of A's = 1,065,083,337 bp (28.64%) number of C's = 755,383,027 bp (20.31%) number of T's = 1,068,976,684 bp (28.74%) number of G's = 829,452,277 bp (22.3%) number of N's = 253,976 bp (0.01%) GC percentage = 42.61% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 35,347,666 number of insertions = 584,823 mapped reads with insertion percentage = 1.47% number of deletions = 2,019,173 mapped reads with deletion percentage = 5.02% homopolymer indels = 53.14% >>>>>>> Coverage mean coverageData = 1.2023X std coverageData = 5.3798X There is a 37.24% of reference with a coverageData >= 1X There is a 23.89% of reference with a coverageData >= 2X There is a 15.57% of reference with a coverageData >= 3X There is a 10.78% of reference with a coverageData >= 4X There is a 7.65% of reference with a coverageData >= 5X There is a 5.56% of reference with a coverageData >= 6X There is a 4.11% of reference with a coverageData >= 7X There is a 3.08% of reference with a coverageData >= 8X There is a 2.33% of reference with a coverageData >= 9X There is a 1.78% of reference with a coverageData >= 10X There is a 1.37% of reference with a coverageData >= 11X There is a 1.06% of reference with a coverageData >= 12X There is a 0.83% of reference with a coverageData >= 13X There is a 0.65% of reference with a coverageData >= 14X There is a 0.51% of reference with a coverageData >= 15X There is a 0.41% of reference with a coverageData >= 16X There is a 0.32% of reference with a coverageData >= 17X There is a 0.26% of reference with a coverageData >= 18X There is a 0.21% of reference with a coverageData >= 19X There is a 0.17% of reference with a coverageData >= 20X There is a 0.14% of reference with a coverageData >= 21X There is a 0.11% of reference with a coverageData >= 22X There is a 0.09% of reference with a coverageData >= 23X There is a 0.08% of reference with a coverageData >= 24X There is a 0.06% of reference with a coverageData >= 25X There is a 0.05% of reference with a coverageData >= 26X There is a 0.05% of reference with a coverageData >= 27X There is a 0.04% of reference with a coverageData >= 28X There is a 0.03% 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 0.02% 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 0.01% 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 306241181 1.2286476148839767 4.692287985674443 chr2 243199373 322076765 1.3243322177479462 6.338175848437393 chr3 198022430 251601001 1.2705681927042305 2.763357240378815 chr4 191154276 217342503 1.1370004770387663 2.620376616604802 chr5 180915260 223229587 1.2338903141725026 2.4711868358873947 chr6 171115067 213225812 1.2460960670400814 2.5325931178329197 chr7 159138663 191393753 1.2026854404325364 3.1948603630791026 chr8 146364022 188775829 1.2897693464586537 2.9292409178441963 chr9 141213431 158240262 1.1205751526566903 4.5384313690984595 chr10 135534747 193475618 1.4274982783566195 18.920444809953068 chr11 135006516 178637305 1.3231754310288253 3.330943060607449 chr12 133851895 166044682 1.240510506033553 2.8345398606667174 chr13 115169878 111806113 0.9707930141247523 2.317712310831494 chr14 107349540 113718655 1.0593306221899041 2.4201828296047876 chr15 102531392 111730744 1.0897222969527225 2.526051769744256 chr16 90354753 119920398 1.3272173739437925 7.082434360312392 chr17 81195210 98163075 1.208976182215675 3.0089469746877677 chr18 78077248 100186094 1.2831663072960768 4.824401024639116 chr19 59128983 60909592 1.0301139798058085 3.1538548849151824 chr20 63025520 89348281 1.4176524207971628 2.9307576369863764 chr21 48129895 46585687 0.967915824457959 3.252589261330106 chr22 51304566 48761496 0.9504318972311353 2.4279577731500153 chrMT 16571 42088 2.5398587894514515 2.652177030901588 chrX 155270560 205463965 1.3232641461459276 2.798882258251232 chrY 59373566 5060234 0.08522705205208661 1.703076830316904