BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716114.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 = 1,349,194 number of mapped reads = 1,164,497 (86.31%) number of supplementary alignments = 3,359 (0.25%) number of secondary alignments = 0 number of mapped bases = 65,826,925 bp number of sequenced bases = 65,808,282 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,895 duplication rate = 1.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.6176 >>>>>>> ACTG content number of A's = 14,845,740 bp (22.56%) number of C's = 13,655,830 bp (20.75%) number of T's = 19,840,788 bp (30.15%) number of G's = 17,463,995 bp (26.54%) number of N's = 1,929 bp (0%) GC percentage = 47.29% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 341,854 number of insertions = 4,449 mapped reads with insertion percentage = 0.38% number of deletions = 10,990 mapped reads with deletion percentage = 0.94% homopolymer indels = 38.69% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 0.1875X There is a 1.92% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6503679 0.026092929975087203 0.24243990974890228 chr2 243199373 5654326 0.023249755664460532 0.21733584017309313 chr3 198022430 4430833 0.022375409694750235 0.16569946247979966 chr4 191154276 4112830 0.021515762482864888 0.18097031208401843 chr5 180915260 4021347 0.022227793277360904 0.16162670005609117 chr6 171115067 2821164 0.016486940919118478 0.14339257177691542 chr7 159138663 3849892 0.024192059474572813 0.21906325084717218 chr8 146364022 4046853 0.02764923336146092 0.19061270549143267 chr9 141213431 2913579 0.02063244961451294 0.16968803218852158 chr10 135534747 3474783 0.025637580597689832 0.2847612772010386 chr11 135006516 2714641 0.020107481330752953 0.1838591036402121 chr12 133851895 3137497 0.023440064109663893 0.16790773028390346 chr13 115169878 1168782 0.010148330625130991 0.10978192678492439 chr14 107349540 2043513 0.0190360666659587 0.1530023531302244 chr15 102531392 1310084 0.012777394068735553 0.12464131610483405 chr16 90354753 1762771 0.019509444068758618 0.1660621979879559 chr17 81195210 2628499 0.03237258700359295 0.20578194248182505 chr18 78077248 1748687 0.022396883148340475 0.21282516198963128 chr19 59128983 1805403 0.030533300395171686 0.2301322037098521 chr20 63025520 1706496 0.027076270056954708 0.18687589340426083 chr21 48129895 894976 0.01859501251768781 0.16467801701395576 chr22 51304566 721036 0.014054031760058159 0.129905620826429 chrMT 16571 50288 3.034699173254481 2.858053803586332 chrX 155270560 2108927 0.013582272131948259 0.1360892800420208 chrY 59373566 196039 0.003301789217107155 0.10363253257471533