BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716384.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 = 749,396 number of mapped reads = 664,567 (88.68%) number of supplementary alignments = 2,840 (0.38%) number of secondary alignments = 0 number of mapped bases = 38,405,468 bp number of sequenced bases = 38,393,924 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,109 duplication rate = 1.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5557 >>>>>>> ACTG content number of A's = 9,870,826 bp (25.71%) number of C's = 7,874,165 bp (20.51%) number of T's = 11,673,235 bp (30.4%) number of G's = 8,975,439 bp (23.38%) number of N's = 259 bp (0%) GC percentage = 43.89% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 195,818 number of insertions = 2,974 mapped reads with insertion percentage = 0.45% number of deletions = 7,156 mapped reads with deletion percentage = 1.07% homopolymer indels = 38.93% >>>>>>> Coverage mean coverageData = 0.0124X std coverageData = 0.1356X There is a 1.18% 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 3255109 0.013059582306918305 0.17306565523795436 chr2 243199373 3008348 0.01236988386479105 0.15801591083593805 chr3 198022430 2245725 0.011340760741093825 0.11241732308481765 chr4 191154276 2369205 0.012394203517581788 0.12154384870492811 chr5 180915260 2175531 0.012025138177951379 0.11329326629012935 chr6 171115067 2072908 0.012114117338363898 0.12330658064255556 chr7 159138663 2177187 0.013681068817324423 0.1721546038632871 chr8 146364022 1990779 0.013601559815020661 0.13669267308080982 chr9 141213431 1276142 0.009036973260709175 0.10743418228770568 chr10 135534747 1705925 0.012586624742067065 0.17127825268699187 chr11 135006516 1346306 0.009972155714321225 0.11527176085019374 chr12 133851895 1907310 0.014249406031942993 0.12424141689500984 chr13 115169878 1161397 0.01008420795583373 0.10422723234778601 chr14 107349540 1294747 0.012061039106455416 0.1163496247031974 chr15 102531392 1434658 0.013992378061150286 0.12472346530901231 chr16 90354753 1345589 0.01489228795744702 0.13293249606847676 chr17 81195210 1668054 0.020543748824591992 0.1527868576222411 chr18 78077248 714004 0.009144840760780914 0.1464715819516664 chr19 59128983 994434 0.0168180467436756 0.17381025982469125 chr20 63025520 1215819 0.019290899940214695 0.14695464072998635 chr21 48129895 482130 0.010017266815146803 0.10810660971922466 chr22 51304566 356333 0.00694544419301783 0.08631063443958856 chrMT 16571 1450 0.08750226298956007 0.3162298383185861 chrX 155270560 2082844 0.013414287937133736 0.12307363952855198 chrY 59373566 123534 0.0020806228819067393 0.0733682740716791