BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124793.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 412,663 number of mapped reads = 404,446 (98.01%) number of supplementary alignments = 106,665 (25.85%) number of secondary alignments = 0 number of mapped bases = 57,988,062 bp number of sequenced bases = 57,949,406 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 442,918 duplication rate = 1.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.9011 >>>>>>> ACTG content number of A's = 17,018,263 bp (29.37%) number of C's = 10,731,861 bp (18.52%) number of T's = 17,527,765 bp (30.25%) number of G's = 12,671,517 bp (21.87%) number of N's = 0 bp (0%) GC percentage = 40.39% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 571,126 number of insertions = 5,893 mapped reads with insertion percentage = 1.41% number of deletions = 32,740 mapped reads with deletion percentage = 8.01% homopolymer indels = 68.6% >>>>>>> Coverage mean coverageData = 0.0187X std coverageData = 30.4044X There is a 0.26% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% 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 10293683 0.04129852498943222 35.75239967419128 chr2 243199373 6767703 0.027827797894857238 23.90157266565864 chr3 198022430 705830 0.0035643941951424393 0.8473890455413654 chr4 191154276 1224708 0.006406908731667609 2.038262974470895 chr5 180915260 549516 0.003037422050522438 0.10971635090376583 chr6 171115067 479473 0.002802050154940476 0.060202341016562536 chr7 159138663 457620 0.0028756054083475618 0.08872601034478804 chr8 146364022 948059 0.006477404672577254 2.3294828424715437 chr9 141213431 376346 0.0026650864392636984 0.19060341693322955 chr10 135534747 31925919 0.23555523367007872 133.12045183301439 chr11 135006516 397466 0.002944050493088793 0.07339740533068512 chr12 133851895 383350 0.002863986348493609 0.05497390244044535 chr13 115169878 443429 0.0038502168075579624 0.7849649850230764 chr14 107349540 467868 0.004358360548168161 1.4920913939172078 chr15 102531392 711240 0.00693680234049685 1.7712646050584797 chr16 90354753 296029 0.0032762969314962323 0.0844028205247366 chr17 81195210 292978 0.0036083163033878477 0.3099727572845506 chr18 78077248 229529 0.0029397680614972493 0.06453140179270864 chr19 59128983 200825 0.0033963885358894133 0.19185855677860877 chr20 63025520 196015 0.0031100893733205215 0.06866282784121318 chr21 48129895 112532 0.0023380894556283573 0.05145113200362662 chr22 51304566 110214 0.0021482298476123937 0.09514616708817626 chrMT 16571 5939 0.35839719992758434 0.6051535273980402 chrX 155270560 279215 0.0017982481675856647 0.08712419037265405 chrY 59373566 132576 0.0022329128757400223 0.08763876575278569