BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716496.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 = 1,256,426 number of mapped reads = 1,080,733 (86.02%) number of supplementary alignments = 4,974 (0.4%) number of secondary alignments = 0 number of mapped bases = 62,567,372 bp number of sequenced bases = 62,549,887 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,771 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7271 >>>>>>> ACTG content number of A's = 15,633,178 bp (24.99%) number of C's = 11,563,838 bp (18.49%) number of T's = 20,210,659 bp (32.31%) number of G's = 15,140,576 bp (24.21%) number of N's = 1,636 bp (0%) GC percentage = 42.69% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 305,026 number of insertions = 4,368 mapped reads with insertion percentage = 0.4% number of deletions = 11,177 mapped reads with deletion percentage = 1.03% homopolymer indels = 44.05% >>>>>>> Coverage mean coverageData = 0.0202X std coverageData = 0.2084X There is a 1.86% of reference with a coverageData >= 1X There is a 0.12% 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 6990339 0.02804542260297919 0.37066582270566056 chr2 243199373 5243122 0.021558945384287646 0.2555396790259312 chr3 198022430 6012911 0.030364797563589136 0.18723743652656402 chr4 191154276 2871406 0.015021406060516272 0.13783134335333988 chr5 180915260 2725984 0.015067739448844724 0.13225488161239862 chr6 171115067 4617769 0.026986337795724322 0.23336954354336825 chr7 159138663 3534204 0.02220833035401334 0.24852853184131463 chr8 146364022 4782996 0.032678768556934024 0.21161086692911793 chr9 141213431 2289196 0.016210894273930642 0.17143039046037958 chr10 135534747 3251379 0.023989265276748554 0.2278242143505909 chr11 135006516 2038829 0.01510170812792473 0.15717966983210707 chr12 133851895 2715964 0.02029081470979548 0.15532013120939386 chr13 115169878 1396186 0.01212283996688787 0.11694205772110897 chr14 107349540 1350551 0.012580873658145158 0.12953764605789456 chr15 102531392 1810525 0.01765825046050287 0.14279843882196183 chr16 90354753 1289325 0.0142695869026392 0.13769161355705598 chr17 81195210 1315754 0.01620482291997274 0.13933753991756573 chr18 78077248 1184387 0.015169425541228092 0.26346601940961484 chr19 59128983 1146988 0.01939806744181614 0.2690281946502073 chr20 63025520 932642 0.014797846967387179 0.13010004592605953 chr21 48129895 566995 0.01178051603894004 0.1273145449141165 chr22 51304566 943784 0.018395711601965407 0.14481049305583787 chrMT 16571 96062 5.79699474986422 3.8379255715488734 chrX 155270560 3308206 0.021306073733488178 0.17187315595302965 chrY 59373566 151868 0.002557838617946579 0.06970165341378826