BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006189.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 = 7,589,956 number of mapped reads = 6,443,589 (84.9%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 3,245,233 number of mapped paired reads (second in pair) = 3,198,356 number of mapped paired reads (both in pair) = 5,975,700 number of mapped paired reads (singletons) = 467,889 number of mapped bases = 249,430,318 bp number of sequenced bases = 249,398,963 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 216,659 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 50,250.1167 std insert size = 2,125,720.7537 median insert size = 104 >>>>>>> Mapping quality mean mapping quality = 47.6731 >>>>>>> ACTG content number of A's = 67,686,015 bp (27.14%) number of C's = 55,395,677 bp (22.21%) number of T's = 69,059,146 bp (27.69%) number of G's = 57,228,315 bp (22.95%) number of N's = 29,810 bp (0.01%) GC percentage = 45.16% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 777,008 number of insertions = 7,344 mapped reads with insertion percentage = 0.11% number of deletions = 23,541 mapped reads with deletion percentage = 0.37% homopolymer indels = 43.29% >>>>>>> Coverage mean coverageData = 0.0806X std coverageData = 0.4487X There is a 6.37% of reference with a coverageData >= 1X There is a 1.23% of reference with a coverageData >= 2X There is a 0.26% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% 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% 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 20604571 0.0826660768881294 0.528335097019497 chr2 243199373 20889109 0.08589293937036589 0.42970997557402785 chr3 198022430 16979729 0.08574649346541198 0.35207426125038915 chr4 191154276 16056031 0.08399514431997325 0.41236656507444763 chr5 180915260 14646581 0.08095823978585333 0.34215316587758227 chr6 171115067 13830199 0.08082396975597712 0.369058203046488 chr7 159138663 13059486 0.08206356490502877 0.4606336278328193 chr8 146364022 12445402 0.08503047285759885 0.7976311428363635 chr9 141213431 10491342 0.07429422205597426 0.3697097853398271 chr10 135534747 11951919 0.08818343092491256 0.4976863580520225 chr11 135006516 11311681 0.08378618554974043 0.406478217504136 chr12 133851895 11220000 0.08382399068761784 0.35063445114378256 chr13 115169878 7586836 0.0658751761463184 0.31019050800297915 chr14 107349540 7655004 0.0713091458053756 0.7211946956505888 chr15 102531392 7333957 0.07152889331688776 0.32517616309621966 chr16 90354753 7782428 0.08613191604873294 0.40940180230139217 chr17 81195210 7003095 0.08625010022142932 0.3692500441912406 chr18 78077248 6239874 0.07991923588290407 0.5226498463373128 chr19 59128983 5356036 0.09058224458215357 0.4713684125710869 chr20 63025520 5613378 0.08906515963692167 0.3851411583688419 chr21 48129895 3253314 0.06759445454846723 0.39103217012266384 chr22 51304566 3574474 0.0696716545657944 0.3480259582741759 chrMT 16571 4111 0.24808400217246998 0.6963410612902455 chrX 155270560 13857457 0.08924716314541534 0.37857973634166553 chrY 59373566 684304 0.011525398356568309 0.2836558362104955