BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006404.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 9,629,344 number of mapped reads = 8,594,001 (89.25%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,322,727 number of mapped paired reads (second in pair) = 4,271,274 number of mapped paired reads (both in pair) = 7,953,260 number of mapped paired reads (singletons) = 640,741 number of mapped bases = 332,908,441 bp number of sequenced bases = 332,866,334 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 319,421 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 63,835.3626 std insert size = 2,385,905.7853 median insert size = 138 >>>>>>> Mapping quality mean mapping quality = 48.2738 >>>>>>> ACTG content number of A's = 92,255,975 bp (27.72%) number of C's = 72,135,333 bp (21.67%) number of T's = 94,062,252 bp (28.26%) number of G's = 74,397,976 bp (22.35%) number of N's = 14,798 bp (0%) GC percentage = 44.02% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 990,955 number of insertions = 9,385 mapped reads with insertion percentage = 0.11% number of deletions = 31,767 mapped reads with deletion percentage = 0.37% homopolymer indels = 44.98% >>>>>>> Coverage mean coverageData = 0.1075X std coverageData = 0.538X There is a 8.48% of reference with a coverageData >= 1X There is a 1.64% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 27268243 0.10940090295702815 0.744728055513794 chr2 243199373 28265846 0.11622499536625039 0.5229161243302688 chr3 198022430 22801691 0.11514701137643851 0.40620632766014714 chr4 191154276 20433352 0.10689455882221541 0.43705339293139917 chr5 180915260 19954792 0.11029910909671191 0.399386241591028 chr6 171115067 19027039 0.11119441048402827 0.4524912107069216 chr7 159138663 17822761 0.1119951661275425 0.6171648155096342 chr8 146364022 16589197 0.11334204111991401 1.031971570371111 chr9 141213431 14041938 0.09943769442157382 0.45294157397991436 chr10 135534747 15766351 0.11632700358381161 0.5464463544957584 chr11 135006516 15371468 0.11385723041693781 0.5081390095695619 chr12 133851895 14388169 0.10749320358893687 0.3980512095123374 chr13 115169878 10422412 0.09049598889042845 0.3597162532891099 chr14 107349540 10277346 0.09573721508261702 0.46215405215688954 chr15 102531392 9566780 0.09330586285222774 0.36921509411168607 chr16 90354753 10539915 0.11665036591932247 0.48029976676104125 chr17 81195210 9224969 0.1136146947584716 0.43311633600323707 chr18 78077248 8907510 0.11408586019835125 0.7267677393353267 chr19 59128983 7052744 0.11927727557905063 0.5973913045609269 chr20 63025520 7449942 0.11820516514580126 0.4339412153839898 chr21 48129895 4516301 0.09383567115614942 0.4425710993216115 chr22 51304566 4320013 0.08420328514230098 0.36639725618929075 chrMT 16571 7243 0.43708889022991976 1.447930883066506 chrX 155270560 18115027 0.11666749318093526 0.4557777037071074 chrY 59373566 777392 0.013093234117014296 0.2836938727745597