BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240021.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 = 2,203,882 number of mapped reads = 1,464,122 (66.43%) number of supplementary alignments = 4,729 (0.21%) number of secondary alignments = 0 number of mapped bases = 88,980,275 bp number of sequenced bases = 88,926,974 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,340 duplication rate = 6.77% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9033 >>>>>>> ACTG content number of A's = 23,548,380 bp (26.48%) number of C's = 15,038,003 bp (16.91%) number of T's = 29,106,982 bp (32.73%) number of G's = 21,177,313 bp (23.81%) number of N's = 56,296 bp (0.06%) GC percentage = 40.72% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 916,989 number of insertions = 6,426 mapped reads with insertion percentage = 0.44% number of deletions = 31,211 mapped reads with deletion percentage = 2.1% homopolymer indels = 49.5% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 0.2845X There is a 2.25% of reference with a coverageData >= 1X There is a 0.43% of reference with a coverageData >= 2X There is a 0.11% 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 6444695 0.025856284626869595 0.3716183826486543 chr2 243199373 9069312 0.037291675089968265 0.34209419846551753 chr3 198022430 6521440 0.0329328349318812 0.22929476126382314 chr4 191154276 6022215 0.03150447442776535 0.22964164142826068 chr5 180915260 4941338 0.027312997256284516 0.20999161851997292 chr6 171115067 4996440 0.029199298972310838 0.24738456815981696 chr7 159138663 5315956 0.03340455361246814 0.5119167108128774 chr8 146364022 5288005 0.03612913151566715 0.3650676178366022 chr9 141213431 3370036 0.023864840448498133 0.2685859765000515 chr10 135534747 3828546 0.028247708316451133 0.24472554556241446 chr11 135006516 3940981 0.029191042897514664 0.25881561898582595 chr12 133851895 3960834 0.029591168656969705 0.21696900014899048 chr13 115169878 2282105 0.019815120408480418 0.17656470218176973 chr14 107349540 3130045 0.029157507335383085 0.22211245614525857 chr15 102531392 2259680 0.022038908825113775 0.19674952462491435 chr16 90354753 2393916 0.026494632772666647 0.20947201429466045 chr17 81195210 2359514 0.029059768427226188 0.22913755954295054 chr18 78077248 2170235 0.027795997625326137 0.37253655057141477 chr19 59128983 1583114 0.02677390882911008 0.30229910730719134 chr20 63025520 1749114 0.02775247233184272 0.2145315748258307 chr21 48129895 1359551 0.02824753721153973 0.21484822038387666 chr22 51304566 854086 0.016647368189412225 0.1576123730949775 chrMT 16571 55730 3.36310421821254 4.119508180694024 chrX 155270560 4893426 0.031515478529864256 0.2441076567199905 chrY 59373566 189961 0.0031994204289498124 0.07614918415231516