BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818969.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 937,792 number of mapped reads = 902,763 (96.26%) number of supplementary alignments = 13,522 (1.44%) number of secondary alignments = 0 number of mapped bases = 83,616,581 bp number of sequenced bases = 83,569,226 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 293,427 duplication rate = 27.91% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.1394 >>>>>>> ACTG content number of A's = 24,516,353 bp (29.34%) number of C's = 18,016,990 bp (21.56%) number of T's = 24,098,296 bp (28.84%) number of G's = 16,933,702 bp (20.26%) number of N's = 3,885 bp (0%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 504,342 number of insertions = 12,052 mapped reads with insertion percentage = 1.31% number of deletions = 25,792 mapped reads with deletion percentage = 2.8% homopolymer indels = 41.68% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.3442X There is a 1.64% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.05% 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% 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 8407925 0.033732814651643336 0.6027331832202867 chr2 243199373 6829582 0.028082235228460067 0.4242288253145551 chr3 198022430 4475614 0.022601550743519307 0.22576990438980135 chr4 191154276 4744544 0.0248204962990208 0.2530953777291975 chr5 180915260 4715573 0.026065092574280357 0.24790640845032313 chr6 171115067 3575935 0.020897838294976094 0.23598425816154683 chr7 159138663 4113549 0.02584883473603143 0.42095323140675683 chr8 146364022 7909693 0.054041238358426634 0.383367443247143 chr9 141213431 3445961 0.02440250177052918 0.31916185400829133 chr10 135534747 4456314 0.03287949473207782 0.38968586768379193 chr11 135006516 2786935 0.020642966595775275 0.2400700750341636 chr12 133851895 3669411 0.027413963769433374 0.25349823784943276 chr13 115169878 1905845 0.01654812033403387 0.19382944903923385 chr14 107349540 1877727 0.017491709792142564 0.2086124676164185 chr15 102531392 2167676 0.021141583642988092 0.2186693227182491 chr16 90354753 2590244 0.028667490242599635 0.35117539048179747 chr17 81195210 2858238 0.035202051943704564 0.30370226507730896 chr18 78077248 1898085 0.024310347106496377 0.3542070773450646 chr19 59128983 1651747 0.027934642474740347 0.5414824269040448 chr20 63025520 2380908 0.0377768878384502 0.3117180748887973 chr21 48129895 1182532 0.024569594427746 0.2474147593646653 chr22 51304566 668598 0.013031939496379328 0.18329083596913448 chrMT 16571 10023 0.6048518496168004 1.2167434585629413 chrX 155270560 5013893 0.032291330693983454 0.30293155477545153 chrY 59373566 280029 0.00471639180304582 0.24279901863852257