BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004066.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 = 2,942,814 number of mapped reads = 2,428,895 (82.54%) number of supplementary alignments = 25,634 (0.87%) number of secondary alignments = 0 number of mapped bases = 154,989,652 bp number of sequenced bases = 154,902,519 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 209,992 duplication rate = 6.87% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8994 >>>>>>> ACTG content number of A's = 42,906,178 bp (27.7%) number of C's = 27,616,286 bp (17.83%) number of T's = 49,984,336 bp (32.27%) number of G's = 34,282,450 bp (22.13%) number of N's = 113,269 bp (0.07%) GC percentage = 39.96% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 1,423,597 number of insertions = 12,212 mapped reads with insertion percentage = 0.5% number of deletions = 51,552 mapped reads with deletion percentage = 2.1% homopolymer indels = 44.62% >>>>>>> Coverage mean coverageData = 0.0501X std coverageData = 0.4892X There is a 3.55% of reference with a coverageData >= 1X There is a 0.93% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 11435057 0.04587774728152031 0.8937208086256367 chr2 243199373 14095276 0.05795769876429739 0.5521680929742139 chr3 198022430 10207781 0.05154860992262341 0.3033437936347908 chr4 191154276 10593970 0.05542104640128479 0.34156082860018805 chr5 180915260 8834711 0.04883342068546346 0.29653477599421196 chr6 171115067 9395371 0.05490674295794186 0.3911044699614535 chr7 159138663 9684293 0.060854432338670585 0.5596821603753868 chr8 146364022 7600991 0.0519320998161693 0.7127139085546254 chr9 141213431 6416878 0.04544098924981151 0.4234602092922382 chr10 135534747 7522780 0.05550443828253134 0.4768497656721403 chr11 135006516 7033485 0.05209737432228827 0.4119761840777024 chr12 133851895 5930098 0.04430342954800901 0.2881553769098432 chr13 115169878 5731660 0.04976700591798838 0.2977266909397891 chr14 107349540 4542820 0.04231802017968591 0.3094044206747786 chr15 102531392 4828115 0.04708913929501708 0.3108792530554784 chr16 90354753 4459950 0.04936043596953887 0.3530047400426549 chr17 81195210 3661494 0.045094950798205954 0.34271061718266427 chr18 78077248 4339975 0.05558565537555832 0.8452664298949224 chr19 59128983 2435975 0.04119764752253561 0.6131499818588535 chr20 63025520 2683711 0.04258133848003158 0.28655251071539134 chr21 48129895 2074839 0.043109152845648216 0.3044282003704054 chr22 51304566 1354457 0.026400320782364674 0.20999126415130348 chrMT 16571 257332 15.529056785951362 9.452870729122214 chrX 155270560 9401281 0.06054773680213429 0.3698951935928162 chrY 59373566 467352 0.007871381685243565 0.20398489787298005