BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004024.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 = 2,015,664 number of mapped reads = 789,442 (39.17%) number of supplementary alignments = 6,771 (0.34%) number of secondary alignments = 0 number of mapped bases = 49,927,459 bp number of sequenced bases = 49,899,496 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 133,379 duplication rate = 12.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.4182 >>>>>>> ACTG content number of A's = 13,437,634 bp (26.93%) number of C's = 9,282,437 bp (18.6%) number of T's = 15,684,165 bp (31.43%) number of G's = 11,485,648 bp (23.02%) number of N's = 9,612 bp (0.02%) GC percentage = 41.62% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 523,504 number of insertions = 3,995 mapped reads with insertion percentage = 0.5% number of deletions = 16,812 mapped reads with deletion percentage = 2.1% homopolymer indels = 47% >>>>>>> Coverage mean coverageData = 0.0161X std coverageData = 0.2633X There is a 0.78% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.2% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 4743182 0.019029770040171735 0.31648051191941673 chr2 243199373 4487228 0.018450820594837637 0.3172035172417093 chr3 198022430 3163175 0.0159738217534246 0.24047740943833804 chr4 191154276 3214833 0.016818002020525035 0.25639685629605447 chr5 180915260 2483177 0.013725635969016655 0.21619098362825762 chr6 171115067 2781449 0.016254845635539507 0.2502704142007833 chr7 159138663 3268030 0.020535738697264286 0.3374472246389735 chr8 146364022 2755172 0.01882410692430958 0.29663771304674996 chr9 141213431 1771732 0.01254648362732579 0.2196528666154229 chr10 135534747 2442683 0.018022559189194487 0.2622599314098766 chr11 135006516 2134520 0.015810496139312267 0.2558714258325947 chr12 133851895 2061273 0.015399654969397332 0.23185293858764297 chr13 115169878 1301771 0.011303050959210012 0.19674511211057322 chr14 107349540 1408016 0.013116181028814842 0.23822149248172758 chr15 102531392 1325344 0.012926226535576539 0.23100776485047977 chr16 90354753 1434059 0.01587142847925222 0.24284026353116445 chr17 81195210 1477056 0.018191417942018992 0.24797275315056172 chr18 78077248 1319414 0.016898828196403645 0.3114057461293946 chr19 59128983 1071547 0.018122195675173376 0.29007630756015984 chr20 63025520 812422 0.012890365680441827 0.21210590842023022 chr21 48129895 843950 0.017534839832914657 0.2981756540903765 chr22 51304566 548462 0.010690315555929272 0.1909053851724151 chrMT 16571 15288 0.9225755838513064 1.616017129179558 chrX 155270560 2932447 0.018886046395401677 0.2605272794533019 chrY 59373566 131229 0.0022102260120269684 0.0746021265263234