BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240048.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 = 1,916,485 number of mapped reads = 1,586,350 (82.77%) number of supplementary alignments = 9,316 (0.49%) number of secondary alignments = 0 number of mapped bases = 100,342,671 bp number of sequenced bases = 100,289,836 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 185,176 duplication rate = 9.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8411 >>>>>>> ACTG content number of A's = 27,289,489 bp (27.21%) number of C's = 17,584,367 bp (17.53%) number of T's = 32,819,155 bp (32.72%) number of G's = 22,529,742 bp (22.46%) number of N's = 67,083 bp (0.07%) GC percentage = 40% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 934,270 number of insertions = 7,197 mapped reads with insertion percentage = 0.45% number of deletions = 31,097 mapped reads with deletion percentage = 1.94% homopolymer indels = 49.17% >>>>>>> Coverage mean coverageData = 0.0324X std coverageData = 0.3235X There is a 2.12% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.24% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 6696155 0.026865148713109927 0.3476763021056788 chr2 243199373 12144527 0.049936506209660336 0.4184291528248112 chr3 198022430 5684081 0.028704228101836746 0.24012700408010826 chr4 191154276 5823359 0.030464183809312224 0.2600589773578517 chr5 180915260 6671783 0.03687794495610818 0.2755296614709369 chr6 171115067 5226679 0.03054482046282926 0.2849777184453776 chr7 159138663 4874405 0.0306299230376216 0.4550570041477377 chr8 146364022 6590074 0.045025231678861626 0.5106289888425574 chr9 141213431 3003595 0.021269896062506972 0.2624369030431241 chr10 135534747 5502399 0.04059770001267646 0.32978948001823594 chr11 135006516 5665128 0.041961885750758876 0.40492691088886246 chr12 133851895 6116751 0.045697903641932006 0.30878331537610465 chr13 115169878 1945481 0.016892272821544537 0.18420732440568152 chr14 107349540 4036306 0.03759965808889353 0.2830970689672163 chr15 102531392 2413544 0.02353956142524623 0.22496932954569407 chr16 90354753 2565873 0.028397764531546004 0.2425396532918737 chr17 81195210 2438814 0.03003642702568292 0.2741797567753183 chr18 78077248 2566476 0.03287098438715463 0.44650665335487266 chr19 59128983 1528280 0.025846546354433324 0.2832514587840517 chr20 63025520 1638065 0.025990503529363978 0.22951115206525985 chr21 48129895 1490362 0.03096541141425719 0.2571941720595856 chr22 51304566 948639 0.01849034255547547 0.1893970995814788 chrMT 16571 21452 1.2945507211393399 1.66361901131194 chrX 155270560 4536238 0.02921505532021009 0.25744412383974236 chrY 59373566 214205 0.0036077502907607066 0.08924164146927485