BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1006220.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 = 1,765,066 number of mapped reads = 1,553,561 (88.02%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 777,928 number of mapped paired reads (second in pair) = 775,633 number of mapped paired reads (both in pair) = 1,433,516 number of mapped paired reads (singletons) = 120,045 number of mapped bases = 60,144,755 bp number of sequenced bases = 60,136,780 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 30,323 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 66,426.6845 std insert size = 2,492,739.1357 median insert size = 151 >>>>>>> Mapping quality mean mapping quality = 47.9633 >>>>>>> ACTG content number of A's = 16,540,065 bp (27.5%) number of C's = 13,058,566 bp (21.71%) number of T's = 16,931,513 bp (28.16%) number of G's = 13,603,550 bp (22.62%) number of N's = 3,086 bp (0.01%) GC percentage = 44.34% >>>>>>> Mismatches and indels general error rate = 0.003 number of mismatches = 176,547 number of insertions = 1,794 mapped reads with insertion percentage = 0.12% number of deletions = 6,048 mapped reads with deletion percentage = 0.39% homopolymer indels = 45.45% >>>>>>> Coverage mean coverageData = 0.0194X std coverageData = 0.1647X There is a 1.77% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% 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 4949689 0.01985828151657845 0.18384105802340145 chr2 243199373 5204911 0.021401827380533586 0.16965039987870095 chr3 198022430 4009245 0.02024641854965622 0.15247533543841696 chr4 191154276 3767642 0.019709954068723005 0.1607148671122176 chr5 180915260 3622005 0.020020450458407987 0.1516553298371021 chr6 171115067 3363448 0.019656059860584923 0.1538672962840553 chr7 159138663 3258711 0.02047717970333834 0.17865078384794286 chr8 146364022 2846251 0.019446384166731903 0.23128867620067567 chr9 141213431 2501290 0.017712833561844412 0.1481987761866091 chr10 135534747 2890456 0.021326309776488535 0.1836706850586176 chr11 135006516 2707263 0.020052832116636502 0.15949846813463167 chr12 133851895 2700448 0.020174895544063834 0.1529568310660158 chr13 115169878 1848738 0.016052270195163358 0.13597515724496545 chr14 107349540 1783613 0.01661500366000637 0.15380086975090665 chr15 102531392 1722028 0.016795129437041097 0.13864510177112083 chr16 90354753 1868025 0.020674341282300886 0.16624096220996737 chr17 81195210 1721621 0.021203479860449896 0.1580660531662866 chr18 78077248 1570365 0.02011296555944185 0.18457233518914323 chr19 59128983 1306533 0.022096321189897686 0.17054890422019678 chr20 63025520 1378082 0.021865460213576975 0.16097407156740381 chr21 48129895 781091 0.01622881163567882 0.1473508869370216 chr22 51304566 818437 0.015952517754462634 0.1379084927541249 chrMT 16571 1596 0.09631283567678474 0.36834204525851116 chrX 155270560 3360670 0.021643961353652617 0.16090655113759095 chrY 59373566 162597 0.0027385419295852973 0.08421496916533434