BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237867.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,919,747 number of mapped reads = 1,820,576 (94.83%) number of supplementary alignments = 10,870 (0.57%) number of secondary alignments = 0 number of mapped bases = 130,098,605 bp number of sequenced bases = 130,037,426 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,855 duplication rate = 1.69% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.8154 >>>>>>> ACTG content number of A's = 39,239,802 bp (30.18%) number of C's = 26,042,012 bp (20.03%) number of T's = 38,065,938 bp (29.27%) number of G's = 26,465,382 bp (20.35%) number of N's = 224,292 bp (0.17%) GC percentage = 40.38% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 1,130,185 number of insertions = 8,998 mapped reads with insertion percentage = 0.49% number of deletions = 34,433 mapped reads with deletion percentage = 1.87% homopolymer indels = 46.04% >>>>>>> Coverage mean coverageData = 0.042X std coverageData = 0.5904X There is a 3.2% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 20167840 0.08091390071200665 1.6984047606658852 chr2 243199373 19312469 0.0794100279197677 0.42220433906987054 chr3 198022430 5040485 0.02545411143576008 0.20070646644646625 chr4 191154276 4209042 0.022019083685054473 0.1881234590886513 chr5 180915260 1960157 0.010834669225802179 0.12674213964915199 chr6 171115067 4080742 0.023847940871273482 0.1905312883009315 chr7 159138663 11374138 0.07147312780929924 0.6445235856673375 chr8 146364022 2929420 0.020014618073285795 0.2808194792709582 chr9 141213431 4539392 0.03214561085198758 0.28446719061163045 chr10 135534747 2945302 0.021730973534041423 0.29604462008787924 chr11 135006516 9331390 0.06911807130849892 0.517239497375575 chr12 133851895 5557860 0.041522460328260576 0.25044913381772305 chr13 115169878 12477562 0.10834049854598266 0.4127170254001097 chr14 107349540 895220 0.00833929982373469 0.15368281811139006 chr15 102531392 328330 0.0032022387836107796 0.06497001544355438 chr16 90354753 3102115 0.034332615573637836 0.2933400829566725 chr17 81195210 3269709 0.040269727733938984 0.3134438631401501 chr18 78077248 2964188 0.037964811464666376 0.6666577765925482 chr19 59128983 1102346 0.018643073905059385 0.8394858441098958 chr20 63025520 1140490 0.018095685684148263 0.18540950867404593 chr21 48129895 2109633 0.043832071522283605 0.2802374332924807 chr22 51304566 966735 0.018843059699598666 0.166995100601536 chrMT 16571 64042 3.8647033975016596 3.202434019274879 chrX 155270560 9918896 0.06388136939803657 0.37239639969809196 chrY 59373566 311102 0.005239739179553406 0.10919294055435323