BamQC report ----------------------------------- >>>>>>> Input bam file = SRR926918.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 = 26,257,728 number of mapped reads = 25,076,174 (95.5%) number of supplementary alignments = 827,917 (3.15%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 12,630,702 number of mapped paired reads (second in pair) = 12,445,472 number of mapped paired reads (both in pair) = 24,577,604 number of mapped paired reads (singletons) = 498,570 number of mapped bases = 2,229,912,618 bp number of sequenced bases = 2,228,116,036 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 2,718,647 duplication rate = 8.48% >>>>>>> Insert size mean insert size = 401,970.116 std insert size = 6,222,694.3123 median insert size = 182 >>>>>>> Mapping quality mean mapping quality = 52.4405 >>>>>>> ACTG content number of A's = 636,311,538 bp (28.56%) number of C's = 424,986,616 bp (19.07%) number of T's = 648,920,842 bp (29.12%) number of G's = 517,726,558 bp (23.24%) number of N's = 170,482 bp (0.01%) GC percentage = 42.31% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 23,509,477 number of insertions = 383,070 mapped reads with insertion percentage = 1.5% number of deletions = 1,227,231 mapped reads with deletion percentage = 4.77% homopolymer indels = 51.97% >>>>>>> Coverage mean coverageData = 0.7203X std coverageData = 2.7169X There is a 30.68% of reference with a coverageData >= 1X There is a 15.85% of reference with a coverageData >= 2X There is a 8.7% of reference with a coverageData >= 3X There is a 5.22% of reference with a coverageData >= 4X There is a 3.27% of reference with a coverageData >= 5X There is a 2.13% of reference with a coverageData >= 6X There is a 1.44% of reference with a coverageData >= 7X There is a 0.99% of reference with a coverageData >= 8X There is a 0.7% of reference with a coverageData >= 9X There is a 0.5% of reference with a coverageData >= 10X There is a 0.37% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.21% of reference with a coverageData >= 13X There is a 0.16% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.1% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.06% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.04% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.03% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.02% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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% 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 193410826 0.7759692843453336 2.2736138168291413 chr2 243199373 188019959 0.7731103772212439 3.2044102420291214 chr3 198022430 150348922 0.7592519796873516 1.6920088060323815 chr4 191154276 134586948 0.704075005886868 1.7470881016832889 chr5 180915260 135763940 0.7504283497146675 1.6332995841230742 chr6 171115067 127083441 0.7426782645621732 1.6309408473521334 chr7 159138663 113240100 0.7115813207504451 1.8397557346307618 chr8 146364022 112414786 0.768049309276292 1.7931740158672926 chr9 141213431 96545471 0.6836847622518286 2.5848907165880104 chr10 135534747 111945965 0.8259576785870268 6.480878634191011 chr11 135006516 104875730 0.7768197647586136 2.058601712067112 chr12 133851895 101045592 0.754905950341607 1.7923766856704337 chr13 115169878 67268880 0.5840839737626534 1.453457039827508 chr14 107349540 67391211 0.6277736355460862 1.5529893947991635 chr15 102531392 65473270 0.6385680397277743 1.6201782302922885 chr16 90354753 66983763 0.7413418860212035 3.229860535141787 chr17 81195210 56138976 0.6914074857371513 1.6698465074249407 chr18 78077248 58625014 0.750859123518288 2.4713564283856124 chr19 59128983 34888902 0.5900473884355495 1.6465359650276188 chr20 63025520 50812191 0.8062161327665365 1.8063172497169204 chr21 48129895 28195083 0.5858122690689436 2.015849430111308 chr22 51304566 26682500 0.52008041545464 1.4813897324580454 chrMT 16571 7147354 431.3169995775753 300.7387774129939 chrX 155270560 127470995 0.8209604898700694 1.7888311443713119 chrY 59373566 3552799 0.05983805992047033 1.5111219931401751