BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716584.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 = 1,001,554 number of mapped reads = 922,105 (92.07%) number of supplementary alignments = 5,139 (0.51%) number of secondary alignments = 0 number of mapped bases = 54,031,604 bp number of sequenced bases = 54,015,047 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,079 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7993 >>>>>>> ACTG content number of A's = 13,472,814 bp (24.94%) number of C's = 11,274,240 bp (20.87%) number of T's = 17,024,625 bp (31.52%) number of G's = 12,242,727 bp (22.67%) number of N's = 641 bp (0%) GC percentage = 43.54% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 265,175 number of insertions = 4,270 mapped reads with insertion percentage = 0.46% number of deletions = 10,424 mapped reads with deletion percentage = 1.12% homopolymer indels = 41.69% >>>>>>> Coverage mean coverageData = 0.0175X std coverageData = 0.1777X There is a 1.62% of reference with a coverageData >= 1X There is a 0.09% 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 4521445 0.018140155406072188 0.2516969982939214 chr2 243199373 5348725 0.021993169365613456 0.22722895049017905 chr3 198022430 3703733 0.018703603425127144 0.1449212439056478 chr4 191154276 3028601 0.015843752299843923 0.1467660238075564 chr5 180915260 2925864 0.01617256609530893 0.1334656040016918 chr6 171115067 3036399 0.01774477872249555 0.1466169151716591 chr7 159138663 2620566 0.016467186229910703 0.2581916610687408 chr8 146364022 4526623 0.030927156401864934 0.22547097998238189 chr9 141213431 2201757 0.015591696798302423 0.14450552359343405 chr10 135534747 2590769 0.019115164615314477 0.21281656321463518 chr11 135006516 1841972 0.0136435785069811 0.14041750600229125 chr12 133851895 2535295 0.018941046744239222 0.14879464629910735 chr13 115169878 1404749 0.012197191005099441 0.11617705074796672 chr14 107349540 1769005 0.016478924828182775 0.1373650440564022 chr15 102531392 1310575 0.012782182846010712 0.11991822892287146 chr16 90354753 1666123 0.01843979364317448 0.14714353165208413 chr17 81195210 1893564 0.023321129411451733 0.16436147417954206 chr18 78077248 1297001 0.016611766336846297 0.21761667890667308 chr19 59128983 1109102 0.01875733259271515 0.20864525188787705 chr20 63025520 1260469 0.01999934312323008 0.15158750363565887 chr21 48129895 573599 0.01191772805654365 0.12901190815960317 chr22 51304566 853488 0.01663571230677597 0.1361537889998946 chrMT 16571 8488 0.512220143624404 0.7890967016657217 chrX 155270560 1867947 0.01203027154664735 0.12410370258380712 chrY 59373566 135745 0.0022862867963834277 0.07228231060073058