BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818962.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 = 423,234 number of mapped reads = 407,630 (96.31%) number of supplementary alignments = 6,224 (1.47%) number of secondary alignments = 0 number of mapped bases = 37,639,827 bp number of sequenced bases = 37,615,650 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 62,847 duplication rate = 13.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.7731 >>>>>>> ACTG content number of A's = 11,092,052 bp (29.49%) number of C's = 7,692,523 bp (20.45%) number of T's = 10,577,513 bp (28.12%) number of G's = 8,251,895 bp (21.94%) number of N's = 1,667 bp (0%) GC percentage = 42.39% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 258,072 number of insertions = 5,896 mapped reads with insertion percentage = 1.39% number of deletions = 12,740 mapped reads with deletion percentage = 3.03% homopolymer indels = 39.55% >>>>>>> Coverage mean coverageData = 0.0122X std coverageData = 0.1936X There is a 0.97% of reference with a coverageData >= 1X There is a 0.17% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 3979350 0.015965256110635727 0.32307702420085116 chr2 243199373 3859699 0.01587051377801044 0.2950785256773313 chr3 198022430 1545442 0.007804378524190417 0.10616405027026005 chr4 191154276 2816604 0.01473471616193404 0.15778457484973732 chr5 180915260 1855402 0.01025564123225426 0.125978087589719 chr6 171115067 1861456 0.01087838746543576 0.13568219798477787 chr7 159138663 2318361 0.014568181963423936 0.16980830419428827 chr8 146364022 2358458 0.0161136457428042 0.1669011978254071 chr9 141213431 1632968 0.011563829222448394 0.18882488281569199 chr10 135534747 1689640 0.012466471051884576 0.24441027824095526 chr11 135006516 1640226 0.012149235819106687 0.1447888103443271 chr12 133851895 1659546 0.012398375084641125 0.13716626665665907 chr13 115169878 720668 0.006257434778215186 0.0925234818727517 chr14 107349540 1011068 0.009418466068881153 0.1295411777345353 chr15 102531392 1271386 0.012399968197057151 0.13317009791195097 chr16 90354753 1183943 0.013103273050837735 0.23276640598360823 chr17 81195210 926533 0.011411178073189292 0.13332603924819256 chr18 78077248 826260 0.010582596353805913 0.23529594522124028 chr19 59128983 675924 0.01143134831187609 0.2773273305536975 chr20 63025520 950413 0.015079812114203898 0.1510928019303983 chr21 48129895 551426 0.011457037253042002 0.13789568056476545 chr22 51304566 520981 0.010154671223609999 0.12612095552229796 chrMT 16571 40398 2.437873393277412 2.052901922595044 chrX 155270560 1599789 0.010303234560369976 0.1427597940308812 chrY 59373566 143886 0.0024234016868718987 0.19947508011029366