BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524470.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 = 713,410 number of mapped reads = 663,950 (93.07%) number of supplementary alignments = 1,599 (0.22%) number of secondary alignments = 0 number of mapped bases = 38,977,117 bp number of sequenced bases = 38,964,771 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,494 duplication rate = 1.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4726 >>>>>>> ACTG content number of A's = 9,454,342 bp (24.26%) number of C's = 7,294,583 bp (18.72%) number of T's = 12,397,351 bp (31.82%) number of G's = 9,817,589 bp (25.2%) number of N's = 906 bp (0%) GC percentage = 43.92% >>>>>>> Mismatches and indels general error rate = 0.0047 number of mismatches = 178,305 number of insertions = 2,327 mapped reads with insertion percentage = 0.35% number of deletions = 7,193 mapped reads with deletion percentage = 1.08% homopolymer indels = 43.12% >>>>>>> Coverage mean coverageData = 0.0126X std coverageData = 0.1441X There is a 1.18% of reference with a coverageData >= 1X There is a 0.06% 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 3841105 0.01541061356071807 0.23434934139610109 chr2 243199373 3059915 0.01258191977328823 0.15419346396601694 chr3 198022430 2141165 0.010812739748724425 0.10914885016725362 chr4 191154276 2172938 0.011367456933058614 0.11871383405854355 chr5 180915260 2118143 0.011707928894444835 0.11353616935764309 chr6 171115067 1670155 0.009760420454383483 0.11474590046512528 chr7 159138663 1947963 0.012240664608323371 0.16473956248384478 chr8 146364022 3597578 0.02457966070377596 0.17636513922200578 chr9 141213431 1672884 0.011846493553435438 0.1331773305159987 chr10 135534747 2049632 0.015122557464913406 0.1540342587163341 chr11 135006516 1328878 0.009843065648772093 0.12892409043392117 chr12 133851895 1807235 0.013501751319994386 0.12198036784960364 chr13 115169878 876329 0.007609012141178095 0.09215691087341779 chr14 107349540 922165 0.008590302296591117 0.09728587312573025 chr15 102531392 1045048 0.010192468663645959 0.10827725270551761 chr16 90354753 1222897 0.013534395916062102 0.12580817922169635 chr17 81195210 1343006 0.016540458482710987 0.1379295468052296 chr18 78077248 920639 0.011791386397225476 0.19266028549827893 chr19 59128983 782197 0.013228656410342793 0.17986929459949844 chr20 63025520 1098123 0.017423465923010233 0.13907546414766805 chr21 48129895 541425 0.011249245401428779 0.1146397760197415 chr22 51304566 316666 0.0061722771419604255 0.08239564935493555 chrMT 16571 4634 0.27964516323698024 0.5964310701121828 chrX 155270560 2369555 0.015260813125166806 0.1352622872385582 chrY 59373566 126842 0.002136337911723207 0.06840387399787112