BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716768.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 = 1,234,073 number of mapped reads = 1,078,688 (87.41%) number of supplementary alignments = 4,707 (0.38%) number of secondary alignments = 0 number of mapped bases = 61,064,192 bp number of sequenced bases = 61,046,106 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,384 duplication rate = 1.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.053 >>>>>>> ACTG content number of A's = 14,854,199 bp (24.33%) number of C's = 11,739,871 bp (19.23%) number of T's = 19,403,813 bp (31.79%) number of G's = 15,047,702 bp (24.65%) number of N's = 521 bp (0%) GC percentage = 43.88% >>>>>>> Mismatches and indels general error rate = 0.0054 number of mismatches = 320,011 number of insertions = 4,977 mapped reads with insertion percentage = 0.46% number of deletions = 11,309 mapped reads with deletion percentage = 1.04% homopolymer indels = 38.62% >>>>>>> Coverage mean coverageData = 0.0197X std coverageData = 0.1914X There is a 1.83% of reference with a coverageData >= 1X There is a 0.1% 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 5174069 0.020758499935693238 0.23795239865711296 chr2 243199373 4782045 0.019663064674101772 0.28692501553939065 chr3 198022430 3577072 0.018063973863970864 0.14538534758427907 chr4 191154276 3738112 0.019555471518722396 0.1606365836085925 chr5 180915260 3473746 0.01920095629301807 0.14609909966538562 chr6 171115067 3247245 0.018976967118856925 0.16363314009491384 chr7 159138663 3549822 0.02230647118104794 0.2591862558997539 chr8 146364022 3195633 0.021833459864884008 0.18440288279833095 chr9 141213431 2053041 0.014538567510621565 0.14708562420409504 chr10 135534747 2723749 0.02009631522756301 0.23204105507465017 chr11 135006516 2172959 0.016095215730180017 0.16185661186691458 chr12 133851895 3056227 0.02283290049797203 0.16049404870574985 chr13 115169878 1859498 0.01614569740188489 0.13388416219109794 chr14 107349540 2039489 0.018998581642734567 0.14943685154542602 chr15 102531392 2196096 0.02141876704453598 0.15734528139307644 chr16 90354753 2136075 0.023640981011812407 0.174015254498327 chr17 81195210 2729258 0.033613534591511 0.20214762083555 chr18 78077248 1136672 0.014558300005655937 0.22001689756941234 chr19 59128983 1574692 0.02663147444967893 0.23375728447119679 chr20 63025520 1779024 0.02822704199822548 0.18379335021072998 chr21 48129895 760901 0.01580932183625167 0.1409060301452583 chr22 51304566 575672 0.011220677707321412 0.11291214080189643 chrMT 16571 10451 0.6306801037957879 0.8957582120550994 chrX 155270560 3327532 0.02143054034196824 0.16523099991123197 chrY 59373566 195112 0.0032861762084493967 0.10176235249383524