BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238308.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 = 2,741,633 number of mapped reads = 2,481,835 (90.52%) number of supplementary alignments = 18,468 (0.67%) number of secondary alignments = 0 number of mapped bases = 160,151,508 bp number of sequenced bases = 160,069,360 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,839 duplication rate = 2.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.1229 >>>>>>> ACTG content number of A's = 43,320,434 bp (27.06%) number of C's = 30,706,673 bp (19.18%) number of T's = 48,709,925 bp (30.43%) number of G's = 37,292,927 bp (23.3%) number of N's = 39,401 bp (0.02%) GC percentage = 42.48% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,401,245 number of insertions = 12,863 mapped reads with insertion percentage = 0.51% number of deletions = 49,413 mapped reads with deletion percentage = 1.97% homopolymer indels = 44.36% >>>>>>> Coverage mean coverageData = 0.0517X std coverageData = 0.4348X There is a 4.37% of reference with a coverageData >= 1X There is a 0.57% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 13911499 0.0558132972515242 0.6713252699925593 chr2 243199373 12819491 0.05271185875960297 0.5709178962576826 chr3 198022430 10680293 0.0539347638547815 0.2651130587436648 chr4 191154276 9254723 0.0484149410290984 0.2744332574440135 chr5 180915260 8313955 0.04595496808837463 0.24716618025348203 chr6 171115067 7285428 0.04257619231157476 0.2829496440135151 chr7 159138663 9327530 0.05861259497951167 0.5925179526814481 chr8 146364022 5125574 0.035019357421047094 0.5561462180514594 chr9 141213431 6228972 0.044110336785174495 0.4166021788639583 chr10 135534747 8414957 0.0620870823627243 0.3849385981034821 chr11 135006516 10037795 0.07435044838872815 0.5258016379260285 chr12 133851895 6816381 0.0509248001307714 0.27206618310964914 chr13 115169878 5794956 0.050316594066375585 0.25725489687431213 chr14 107349540 4959599 0.04620046811565285 0.30474344594056296 chr15 102531392 4569884 0.044570583807152446 0.25332219495690556 chr16 90354753 5094584 0.05638423913349638 0.3129496063269862 chr17 81195210 5405364 0.06657244928610936 0.4272427634358329 chr18 78077248 4154993 0.05321643764903189 0.8227663293951074 chr19 59128983 3306158 0.055914338996833415 0.5038823292968291 chr20 63025520 3580590 0.0568117486376947 0.2883257246588491 chr21 48129895 2783300 0.05782892316719162 0.3071012497742387 chr22 51304566 2291269 0.04466013804697227 0.24514151670313183 chrMT 16571 3950 0.23836823366121537 0.5024784516594563 chrX 155270560 9562047 0.061583129474125684 0.33072178796863017 chrY 59373566 428216 0.007212233134186348 0.1633920530896725