BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008776.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,434,916 number of mapped reads = 344,521 (24.01%) number of supplementary alignments = 4,173 (0.29%) number of secondary alignments = 0 number of mapped bases = 22,848,629 bp number of sequenced bases = 22,838,139 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 27,208 duplication rate = 6.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.1901 >>>>>>> ACTG content number of A's = 6,243,276 bp (27.34%) number of C's = 4,279,169 bp (18.74%) number of T's = 7,194,647 bp (31.5%) number of G's = 5,085,518 bp (22.27%) number of N's = 35,529 bp (0.16%) GC percentage = 41% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 198,238 number of insertions = 1,612 mapped reads with insertion percentage = 0.46% number of deletions = 6,140 mapped reads with deletion percentage = 1.77% homopolymer indels = 45.34% >>>>>>> Coverage mean coverageData = 0.0074X std coverageData = 0.1356X There is a 0.5% of reference with a coverageData >= 1X There is a 0.15% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.02% 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 2122685 0.008516267648536772 0.14275893763228523 chr2 243199373 3910123 0.01607784983886451 0.2294014216044085 chr3 198022430 889472 0.004491773987421526 0.09240280399660511 chr4 191154276 885478 0.00463226885910729 0.09569915879850209 chr5 180915260 1042385 0.00576173065776762 0.10780424599625875 chr6 171115067 791371 0.004624788534840126 0.10164214373424209 chr7 159138663 1926181 0.012103790264971624 0.19958296168660308 chr8 146364022 1010605 0.006904736465905535 0.14069160260135088 chr9 141213431 647576 0.004585796091874575 0.10209804946829538 chr10 135534747 1409655 0.010400690828013277 0.15007692789200416 chr11 135006516 1796327 0.013305483714578636 0.17260683066374363 chr12 133851895 618426 0.0046202259594456995 0.09705177668589814 chr13 115169878 420456 0.003650746248077123 0.08335810414354074 chr14 107349540 428467 0.003991325906007609 0.08879958000010084 chr15 102531392 694082 0.0067694584698508725 0.11779562006267655 chr16 90354753 921927 0.010203414534263626 0.14632113747372386 chr17 81195210 344581 0.004243858720237315 0.09020968546454744 chr18 78077248 513310 0.006574386433292321 0.1524030434699129 chr19 59128983 344285 0.0058226098696809985 0.1159166571516477 chr20 63025520 293205 0.004652163123763199 0.09996182544723398 chr21 48129895 737808 0.015329516093895488 0.17745341205572518 chr22 51304566 162300 0.0031634611235187137 0.07671118343628121 chrMT 16571 20355 1.2283507332086174 1.8186816922090459 chrX 155270560 865459 0.005573876979641215 0.10710715037147633 chrY 59373566 52110 8.776633022176906E-4 0.03669877679974941