BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716695.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 = 1,414,041 number of mapped reads = 1,302,926 (92.14%) number of supplementary alignments = 21,528 (1.52%) number of secondary alignments = 0 number of mapped bases = 102,694,155 bp number of sequenced bases = 102,650,699 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 47,153 duplication rate = 2.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.0748 >>>>>>> ACTG content number of A's = 26,020,877 bp (25.35%) number of C's = 20,052,600 bp (19.53%) number of T's = 30,647,743 bp (29.86%) number of G's = 25,923,242 bp (25.25%) number of N's = 6,237 bp (0.01%) GC percentage = 44.79% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 832,805 number of insertions = 9,801 mapped reads with insertion percentage = 0.74% number of deletions = 24,224 mapped reads with deletion percentage = 1.83% homopolymer indels = 42.57% >>>>>>> Coverage mean coverageData = 0.0332X std coverageData = 0.4037X There is a 2.91% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 10542701 0.04229759170790592 0.7375490816914471 chr2 243199373 8900509 0.03659758201761482 0.695565890445024 chr3 198022430 7598938 0.03837412761776532 0.22136658659701472 chr4 191154276 4708205 0.024630393305980765 0.187022797820899 chr5 180915260 5764689 0.031864028495993096 0.1993819380769568 chr6 171115067 7391786 0.04319775066914476 0.28352480537803015 chr7 159138663 5464250 0.03433640761453425 0.5633455669771186 chr8 146364022 4992618 0.03411096478340832 0.47425993053087984 chr9 141213431 4461509 0.031594083993327804 0.3578510241596632 chr10 135534747 5304633 0.03913854651604581 0.405340979733154 chr11 135006516 4063285 0.03009695472772588 0.2924335316845358 chr12 133851895 4566374 0.03411512403317114 0.20926451865108595 chr13 115169878 3604668 0.03129870468387576 0.1951410706776864 chr14 107349540 2562631 0.023871839599871596 0.19335141302091363 chr15 102531392 1853794 0.018080257800459784 0.15386454180833373 chr16 90354753 2928940 0.03241600361632332 0.2192334620968785 chr17 81195210 3738503 0.04604339344648533 0.28670922602344234 chr18 78077248 2487352 0.031857577767085234 0.45305424533413935 chr19 59128983 2345292 0.039664000309289946 0.571512945834348 chr20 63025520 1831096 0.02905324700216674 0.19456633060371056 chr21 48129895 1290410 0.02681098722529937 0.18855041505884018 chr22 51304566 1548802 0.03018838518193488 0.19667324381567416 chrMT 16571 4396 0.2652827228290387 0.5644941120021498 chrX 155270560 4482271 0.028867487822546656 0.23067505884683584 chrY 59373566 256503 0.004320154864877073 0.1379589544447521