BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818817.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 = 196,254 number of mapped reads = 183,108 (93.3%) number of supplementary alignments = 1,683 (0.86%) number of secondary alignments = 0 number of mapped bases = 12,403,271 bp number of sequenced bases = 12,398,500 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 16,490 duplication rate = 8.1% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9172 >>>>>>> ACTG content number of A's = 3,545,081 bp (28.59%) number of C's = 2,440,787 bp (19.69%) number of T's = 3,589,491 bp (28.95%) number of G's = 2,822,436 bp (22.76%) number of N's = 705 bp (0.01%) GC percentage = 42.45% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 64,685 number of insertions = 1,412 mapped reads with insertion percentage = 0.76% number of deletions = 3,078 mapped reads with deletion percentage = 1.66% homopolymer indels = 42.25% >>>>>>> Coverage mean coverageData = 0.004X std coverageData = 0.0808X There is a 0.35% of reference with a coverageData >= 1X There is a 0.04% 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 1080707 0.004335824703923205 0.09848003412508438 chr2 243199373 1107956 0.004555751876876755 0.11550451088429871 chr3 198022430 851652 0.004300785522124943 0.07276612956909093 chr4 191154276 820520 0.004292449100118482 0.0752855411486861 chr5 180915260 753772 0.004166436816883219 0.07228740772401634 chr6 171115067 736213 0.004302444039016155 0.07482128232005726 chr7 159138663 681766 0.0042841003383319864 0.07763130437555596 chr8 146364022 654156 0.004469377044038869 0.07728674278878933 chr9 141213431 526651 0.003729468197681565 0.07234776687096856 chr10 135534747 583760 0.004307087392135686 0.08608175962614144 chr11 135006516 580209 0.00429763701183134 0.07563987394984688 chr12 133851895 560434 0.004186970980126953 0.07353965958180597 chr13 115169878 401239 0.003483888382689786 0.06516178674802636 chr14 107349540 379475 0.0035349476113265134 0.07067165299783691 chr15 102531392 344435 0.0033593126288580964 0.06389462435509151 chr16 90354753 350255 0.0038764424490209163 0.0813205917992715 chr17 81195210 320709 0.0039498512289087 0.07063715708575322 chr18 78077248 326124 0.004176940252812189 0.08662379420145451 chr19 59128983 237570 0.004017826587682051 0.09357377396358318 chr20 63025520 257292 0.004082346325742334 0.07273690836554361 chr21 48129895 168243 0.0034956028888074656 0.066648687319517 chr22 51304566 141221 0.0027526010063119916 0.059747719868294136 chrMT 16571 8590 0.5183754752278076 0.8351255957344084 chrX 155270560 407759 0.002626119207659198 0.05900830109322504 chrY 59373566 122563 0.0020642688027193786 0.10165926613510932