BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717061.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 670,418 number of mapped reads = 522,527 (77.94%) number of supplementary alignments = 2,936 (0.44%) number of secondary alignments = 0 number of mapped bases = 28,952,952 bp number of sequenced bases = 28,944,293 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,668 duplication rate = 1.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.5081 >>>>>>> ACTG content number of A's = 6,968,168 bp (24.07%) number of C's = 6,273,283 bp (21.67%) number of T's = 8,383,814 bp (28.97%) number of G's = 7,318,352 bp (25.28%) number of N's = 676 bp (0%) GC percentage = 46.96% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 157,583 number of insertions = 2,408 mapped reads with insertion percentage = 0.46% number of deletions = 4,923 mapped reads with deletion percentage = 0.93% homopolymer indels = 34.25% >>>>>>> Coverage mean coverageData = 0.0094X std coverageData = 0.1128X There is a 0.88% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% 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 2885375 0.011576199844252344 0.13102963245114488 chr2 243199373 2425626 0.009973816832167573 0.12843506781697628 chr3 198022430 1876225 0.009474810505052382 0.1027237651526177 chr4 191154276 1919072 0.01003938828969748 0.11812937690779164 chr5 180915260 1846968 0.010209022721466393 0.10586853769504373 chr6 171115067 1225034 0.0071591240998082305 0.08902589311049676 chr7 159138663 1731201 0.010878569464920036 0.12324003201129584 chr8 146364022 1798877 0.012290431592539865 0.12011273256683799 chr9 141213431 1258735 0.008913705949117546 0.10391032629198092 chr10 135534747 1493967 0.011022760089705999 0.16805972105116512 chr11 135006516 1159569 0.008588985438302844 0.10891131852896474 chr12 133851895 1371199 0.010244150820576729 0.1058758094996572 chr13 115169878 502058 0.004359282207453585 0.06926571591148048 chr14 107349540 893495 0.008323230821482794 0.09614030003365986 chr15 102531392 572287 0.0055815783716269066 0.07838060902447921 chr16 90354753 782021 0.008655006781989653 0.10323886319631012 chr17 81195210 1155830 0.014235199342424263 0.12934795909397892 chr18 78077248 761228 0.009749677652573 0.12169306679447059 chr19 59128983 781946 0.013224411453178554 0.13365977709337637 chr20 63025520 737272 0.011697991543742915 0.11772358993801081 chr21 48129895 403895 0.008391769813750892 0.10451606750014536 chr22 51304566 337946 0.006587055039116791 0.08655366799945 chrMT 16571 11176 0.6744312352905678 0.9940048817577567 chrX 155270560 920891 0.005930879620708524 0.08468299639039514 chrY 59373566 101059 0.001702087423888267 0.07056442975143677