BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237823.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 = 2,518,093 number of mapped reads = 1,941,682 (77.11%) number of supplementary alignments = 16,324 (0.65%) number of secondary alignments = 0 number of mapped bases = 140,508,423 bp number of sequenced bases = 140,442,014 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 167,754 duplication rate = 7.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.9692 >>>>>>> ACTG content number of A's = 42,178,076 bp (30.03%) number of C's = 27,315,747 bp (19.45%) number of T's = 42,498,594 bp (30.26%) number of G's = 28,203,613 bp (20.08%) number of N's = 245,984 bp (0.18%) GC percentage = 39.53% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,130,106 number of insertions = 10,049 mapped reads with insertion percentage = 0.51% number of deletions = 36,811 mapped reads with deletion percentage = 1.87% homopolymer indels = 46.5% >>>>>>> Coverage mean coverageData = 0.0454X std coverageData = 0.6138X There is a 1.29% of reference with a coverageData >= 1X There is a 0.77% of reference with a coverageData >= 2X There is a 0.56% of reference with a coverageData >= 3X There is a 0.42% of reference with a coverageData >= 4X There is a 0.32% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.2% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 5561435 0.022312622442774176 0.4959664115056782 chr2 243199373 32991177 0.13565486042597652 1.0213317562130924 chr3 198022430 4271384 0.021570202931051802 0.3936506417142622 chr4 191154276 28728486 0.15028952844350707 1.054746414199453 chr5 180915260 3491611 0.01929970418194684 0.402880216231845 chr6 171115067 3494506 0.02042196553036443 0.37830377898705625 chr7 159138663 4135401 0.025986148947349144 0.49875903325321574 chr8 146364022 3233059 0.022089164781219254 0.5641118246230981 chr9 141213431 2986542 0.021149135594616352 0.4849924484244854 chr10 135534747 10487489 0.07737860019025232 0.8437071443204556 chr11 135006516 2653540 0.01965490317519193 0.4257479243294085 chr12 133851895 8741511 0.06530733838321826 0.7093649389405217 chr13 115169878 1882779 0.016347842271744007 0.3333377469083311 chr14 107349540 1952896 0.018191936360416636 0.38875678188442675 chr15 102531392 1437831 0.014023324680893828 0.2947498164162674 chr16 90354753 1842193 0.020388445973616904 0.38363733053116045 chr17 81195210 4007023 0.0493504850840339 0.6044081917660753 chr18 78077248 1512403 0.01937059820551052 0.6793743110522608 chr19 59128983 1388708 0.023486079576237596 0.4435821429847591 chr20 63025520 1629953 0.025861793762272805 0.43205597717257094 chr21 48129895 1614068 0.033535664268538296 0.48397608365877676 chr22 51304566 2546161 0.04962835081774203 0.5952994657901249 chrMT 16571 25599 1.5448071932894816 3.5789838615141782 chrX 155270560 9454713 0.0608918587013533 0.66593283159376 chrY 59373566 437955 0.007376262358909013 0.17725969180883763