BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2046541.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP058890/SRP058890.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 = 176 number of mapped reads = 89 (50.57%) number of supplementary alignments = 1 (0.57%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 64 number of mapped paired reads (second in pair) = 25 number of mapped paired reads (both in pair) = 50 number of mapped paired reads (singletons) = 39 number of mapped bases = 8,332 bp number of sequenced bases = 8,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 5 duplication rate = 5.88% >>>>>>> Insert size mean insert size = 25,909.6087 std insert size = 120,731.4555 median insert size = 140 >>>>>>> Mapping quality mean mapping quality = 6.8962 >>>>>>> ACTG content number of A's = 2,307 bp (27.69%) number of C's = 1,833 bp (22%) number of T's = 2,530 bp (30.36%) number of G's = 1,662 bp (19.95%) number of N's = 0 bp (0%) GC percentage = 41.95% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 44 >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0018X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% 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 1155 4.633890159896532E-6 0.002434284514014764 chr2 243199373 535 2.1998411977813777E-6 0.0016285392706823984 chr3 198022430 443 2.2371203100578053E-6 0.0014956989353979372 chr4 191154276 259 1.3549265306521315E-6 0.0014769841543800294 chr5 180915260 744 4.112422578393885E-6 0.0024410190222302563 chr6 171115067 790 4.616776382409388E-6 0.0023735236834846905 chr7 159138663 96 6.032474961788512E-7 7.766898559085922E-4 chr8 146364022 1241 8.478859647625698E-6 0.0033849168225314843 chr9 141213431 200 1.4162958762753947E-6 0.0015562338971173053 chr10 135534747 497 3.6669563414612786E-6 0.0019379063641402376 chr11 135006516 400 2.96281995751968E-6 0.0017212818418892298 chr12 133851895 452 3.376866648021681E-6 0.002124250154607335 chr13 115169878 397 3.447081883684899E-6 0.0018566286654340405 chr14 107349540 406 3.7820376314607404E-6 0.0022135643118207787 chr15 102531392 100 9.753110540038314E-7 9.875778970654312E-4 chr16 90354753 457 5.057841284785539E-6 0.002852117971301026 chr17 81195210 160 1.9705595933553224E-6 0.0014037648343829573 chr18 78077248 0 0.0 0.0 chr19 59128983 0 0.0 0.0 chr20 63025520 0 0.0 0.0 chr21 48129895 0 0.0 0.0 chr22 51304566 0 0.0 0.0 chrMT 16571 0 0.0 0.0 chrX 155270560 0 0.0 0.0 chrY 59373566 0 0.0 0.0