BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238299.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 = 1,744,561 number of mapped reads = 1,541,577 (88.36%) number of supplementary alignments = 19,840 (1.14%) number of secondary alignments = 0 number of mapped bases = 101,542,257 bp number of sequenced bases = 101,494,710 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 112,049 duplication rate = 6.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.6237 >>>>>>> ACTG content number of A's = 27,667,614 bp (27.26%) number of C's = 18,578,137 bp (18.3%) number of T's = 32,305,955 bp (31.83%) number of G's = 22,861,433 bp (22.52%) number of N's = 81,571 bp (0.08%) GC percentage = 40.83% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 823,891 number of insertions = 7,172 mapped reads with insertion percentage = 0.46% number of deletions = 27,372 mapped reads with deletion percentage = 1.75% homopolymer indels = 46.91% >>>>>>> Coverage mean coverageData = 0.0328X std coverageData = 0.2981X There is a 2.43% of reference with a coverageData >= 1X There is a 0.58% of reference with a coverageData >= 2X There is a 0.15% 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 4852773 0.019469451993862835 0.2874845686549368 chr2 243199373 9137229 0.03757093979021073 0.38292523465265876 chr3 198022430 4374987 0.022093391137559516 0.1895055600291216 chr4 191154276 3684649 0.01927578643336234 0.18624671365285173 chr5 180915260 5378659 0.029730267087475098 0.22218568493484195 chr6 171115067 4590995 0.026829869984505806 0.2442933542467903 chr7 159138663 3593404 0.02258033297665697 0.20601789570846143 chr8 146364022 9091267 0.06211408292674548 0.6356405743479252 chr9 141213431 2468821 0.01748290500781048 0.22717273964255688 chr10 135534747 6847270 0.050520402712671164 0.33905813046086763 chr11 135006516 4043337 0.029949198896444377 0.2346998752291732 chr12 133851895 5498564 0.04107946323808116 0.2639083525507093 chr13 115169878 3425009 0.029738756864880936 0.2237292366384385 chr14 107349540 2813705 0.026210685206475966 0.21395367825252337 chr15 102531392 4023045 0.03923720259254844 0.2582854574713679 chr16 90354753 4889256 0.054111774285963685 0.30591874641116157 chr17 81195210 3350616 0.04126617814031148 0.27211843998810314 chr18 78077248 2844396 0.036430536076271544 0.4229506704195325 chr19 59128983 2368480 0.040056159937673884 0.3727108979737814 chr20 63025520 3459565 0.054891494746889834 0.30658783232936027 chr21 48129895 1521702 0.031616565961758276 0.23238887634341776 chr22 51304566 1357243 0.0264546239412687 0.20545297608201418 chrMT 16571 4242 0.2559893790356647 0.5758562882929831 chrX 155270560 7659336 0.04932896487267129 0.2995938800398295 chrY 59373566 263707 0.004441488321587422 0.13225643759469188