BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124933.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,641,396 number of mapped reads = 4,590,694 (98.91%) number of supplementary alignments = 26,261 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,298,538 number of mapped paired reads (second in pair) = 2,292,156 number of mapped paired reads (both in pair) = 4,574,210 number of mapped paired reads (singletons) = 16,484 number of mapped bases = 407,405,175 bp number of sequenced bases = 407,156,231 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 336,409 duplication rate = 5.3% >>>>>>> Insert size mean insert size = 47,102.7609 std insert size = 2,058,843.4133 median insert size = 189 >>>>>>> Mapping quality mean mapping quality = 52.9797 >>>>>>> ACTG content number of A's = 111,500,054 bp (27.39%) number of C's = 81,175,221 bp (19.94%) number of T's = 117,294,046 bp (28.81%) number of G's = 96,789,395 bp (23.77%) number of N's = 397,515 bp (0.1%) GC percentage = 43.71% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 3,492,232 number of insertions = 58,187 mapped reads with insertion percentage = 1.23% number of deletions = 143,522 mapped reads with deletion percentage = 3.06% homopolymer indels = 47% >>>>>>> Coverage mean coverageData = 0.1316X std coverageData = 1.0627X There is a 9% of reference with a coverageData >= 1X There is a 2.56% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.03% of reference with a coverageData >= 7X There is a 0.02% 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 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% 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 37110565 0.14888855582831226 1.2794283374521171 chr2 243199373 33808868 0.13901708537710744 1.400017482312887 chr3 198022430 28598741 0.14442172535707193 0.49857786794563624 chr4 191154276 15841454 0.08287261123052252 0.8140375080539995 chr5 180915260 22240311 0.12293220041250251 0.47316288399541473 chr6 171115067 22953237 0.13413919301448773 0.8907051825171776 chr7 159138663 34381741 0.21604894971374744 1.747865752083419 chr8 146364022 26582224 0.181617200981263 0.6893771159884464 chr9 141213431 17087194 0.12100261199658834 1.2033321689956986 chr10 135534747 22923453 0.16913340311174963 2.23582090032371 chr11 135006516 14691471 0.10882045871030403 0.713438043035452 chr12 133851895 21166097 0.15813072351347734 0.5311203023794605 chr13 115169878 8701211 0.0755511002625183 0.35056664811660077 chr14 107349540 9665915 0.09004151298645527 0.4215687960922243 chr15 102531392 9081344 0.08857135188411369 0.3915968541077407 chr16 90354753 14457597 0.1600092581737233 1.2689117069965903 chr17 81195210 9872137 0.1215852142016752 1.3680504406728755 chr18 78077248 10481464 0.1342447930541814 1.2715905154857048 chr19 59128983 6235196 0.10545075669574766 0.9606529132990768 chr20 63025520 10458834 0.16594601678812013 0.5779015919080855 chr21 48129895 3896221 0.08095220236819549 0.5046445563694717 chr22 51304566 3950037 0.07699191919877073 0.3833621579536588 chrMT 16571 415379 25.066622412648602 12.995406760969956 chrX 155270560 19577831 0.126088493530261 0.5798086784320237 chrY 59373566 3226653 0.05434494198984107 1.1411221015356718