BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819103.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 = 1,396,882 number of mapped reads = 1,260,911 (90.27%) number of supplementary alignments = 5,029 (0.36%) number of secondary alignments = 0 number of mapped bases = 73,800,940 bp number of sequenced bases = 73,778,485 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 36,596 duplication rate = 2.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7237 >>>>>>> ACTG content number of A's = 18,440,159 bp (24.99%) number of C's = 13,978,049 bp (18.95%) number of T's = 22,192,232 bp (30.08%) number of G's = 19,167,061 bp (25.98%) number of N's = 984 bp (0%) GC percentage = 44.93% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 389,100 number of insertions = 4,181 mapped reads with insertion percentage = 0.33% number of deletions = 13,363 mapped reads with deletion percentage = 1.05% homopolymer indels = 44.79% >>>>>>> Coverage mean coverageData = 0.0238X std coverageData = 0.2319X There is a 2.18% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% 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 7296654 0.029274366381618764 0.4144735505804552 chr2 243199373 5829012 0.023968038766284155 0.25868725231517764 chr3 198022430 4075945 0.02058324907940984 0.15496188373347894 chr4 191154276 4135251 0.021633055176856205 0.17524710684901756 chr5 180915260 4032706 0.02229057957852754 0.16041837532967249 chr6 171115067 3074778 0.017969066394369584 0.17632868757923362 chr7 159138663 3738277 0.02349069000284362 0.29753067910075587 chr8 146364022 6622952 0.04524986338514256 0.25360147086196544 chr9 141213431 3097251 0.021933119095449215 0.19928175082290245 chr10 135534747 3777465 0.02787082341327571 0.24801630774516725 chr11 135006516 2610326 0.01933481492108129 0.2142549262162752 chr12 133851895 3481793 0.026012280214635735 0.17342991952624529 chr13 115169878 1663453 0.014443472797635507 0.12816960257786125 chr14 107349540 1780950 0.01659019684667489 0.139257817232374 chr15 102531392 1969029 0.0192041574935411 0.14929250978090783 chr16 90354753 2362040 0.026141845576181256 0.18731650144232165 chr17 81195210 2627498 0.03236025869013702 0.20179221868016614 chr18 78077248 1713929 0.021951708646288353 0.35744863042183844 chr19 59128983 1562068 0.026417975090151643 0.28847763332702064 chr20 63025520 2114960 0.03355720032139362 0.19862780426743845 chr21 48129895 1043698 0.02168502549195256 0.1669506870395737 chr22 51304566 612096 0.011930634010236049 0.1164019551222648 chrMT 16571 14212 0.857642870074226 1.0539686749566273 chrX 155270560 4320832 0.027827760780923312 0.19430048238300127 chrY 59373566 243765 0.004105614946557193 0.12024655523033531