BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237334.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 = 4,495,173 number of mapped reads = 4,095,359 (91.11%) number of supplementary alignments = 41,409 (0.92%) number of secondary alignments = 0 number of mapped bases = 250,049,000 bp number of sequenced bases = 249,899,789 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,158,300 duplication rate = 21.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.9739 >>>>>>> ACTG content number of A's = 64,777,802 bp (25.92%) number of C's = 42,452,769 bp (16.99%) number of T's = 84,358,412 bp (33.76%) number of G's = 58,284,027 bp (23.32%) number of N's = 26,779 bp (0.01%) GC percentage = 40.31% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 1,638,548 number of insertions = 16,859 mapped reads with insertion percentage = 0.41% number of deletions = 86,036 mapped reads with deletion percentage = 2.07% homopolymer indels = 41.63% >>>>>>> Coverage mean coverageData = 0.0808X std coverageData = 1.2275X There is a 3.77% of reference with a coverageData >= 1X There is a 1.83% of reference with a coverageData >= 2X There is a 0.98% of reference with a coverageData >= 3X There is a 0.53% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.16% of reference with a coverageData >= 6X There is a 0.09% of reference with a coverageData >= 7X There is a 0.06% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% 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 17823777 0.0715094587467447 1.2647817620475388 chr2 243199373 9990314 0.04107869965602255 1.6654451803379624 chr3 198022430 12398232 0.06261024066819097 0.4570502652143335 chr4 191154276 11739648 0.061414519442923685 0.522111206275437 chr5 180915260 10488106 0.057972478385737054 0.45132702920007456 chr6 171115067 27111851 0.15844221946861056 1.3530658951101224 chr7 159138663 33576825 0.21099099594672352 3.2061471614905224 chr8 146364022 16668706 0.11388526888117355 1.2750009618285714 chr9 141213431 17414360 0.12331943127987592 1.084912435515007 chr10 135534747 6632730 0.048937487594970755 0.847122328251206 chr11 135006516 13822623 0.10238485822417638 0.8647460396978702 chr12 133851895 11384597 0.08505368564262762 0.5980702037596355 chr13 115169878 3642886 0.03163054492425528 0.40591379454298937 chr14 107349540 7936915 0.07393524928006212 0.5519267509448303 chr15 102531392 6959037 0.06787225711321661 0.5099427560800548 chr16 90354753 4168531 0.046135160150346494 0.5432940362522243 chr17 81195210 3060253 0.037690068170277535 0.5067088811141418 chr18 78077248 16201897 0.2075111177074274 2.523299656274673 chr19 59128983 1353490 0.02289046642320907 1.5691903206612912 chr20 63025520 5176306 0.08213031800451627 0.5378820879464354 chr21 48129895 4305596 0.08945783073077554 0.5949320672108567 chr22 51304566 2471859 0.04818009765446608 0.37745844278407586 chrMT 16571 10700 0.6457063544746847 1.5125785732382082 chrX 155270560 5034133 0.03242168380148819 0.46679452728863446 chrY 59373566 675628 0.011379272722140354 0.37580820080991945