BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779000.sorted.bam outfile = /home/yangyx/scDNA/SRP052627/SRP052627.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 = 20,601,106 number of mapped reads = 19,924,070 (96.71%) number of supplementary alignments = 108,284 (0.53%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,058,110 number of mapped paired reads (second in pair) = 9,865,960 number of mapped paired reads (both in pair) = 19,659,152 number of mapped paired reads (singletons) = 264,918 number of mapped bases = 1,990,912,565 bp number of sequenced bases = 1,990,428,459 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 429,225 duplication rate = 1.88% >>>>>>> Insert size mean insert size = 77,170.591 std insert size = 2,659,316.8957 median insert size = 278 >>>>>>> Mapping quality mean mapping quality = 53.5169 >>>>>>> ACTG content number of A's = 612,246,795 bp (30.76%) number of C's = 380,772,853 bp (19.13%) number of T's = 609,892,986 bp (30.64%) number of G's = 386,842,030 bp (19.44%) number of N's = 673,795 bp (0.03%) GC percentage = 38.57% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 9,603,225 number of insertions = 175,704 mapped reads with insertion percentage = 0.87% number of deletions = 216,869 mapped reads with deletion percentage = 1.07% homopolymer indels = 47.31% >>>>>>> Coverage mean coverageData = 0.6431X std coverageData = 1.5791X There is a 31.73% of reference with a coverageData >= 1X There is a 14.61% of reference with a coverageData >= 2X There is a 7.31% of reference with a coverageData >= 3X There is a 3.92% of reference with a coverageData >= 4X There is a 2.23% of reference with a coverageData >= 5X There is a 1.33% of reference with a coverageData >= 6X There is a 0.83% of reference with a coverageData >= 7X There is a 0.54% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.13% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.06% of reference with a coverageData >= 15X There is a 0.05% of reference with a coverageData >= 16X There is a 0.04% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% 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 126196850 0.5063050575107695 1.4929259374665969 chr2 243199373 172573878 0.709598367262238 1.5088284868326454 chr3 198022430 156460155 0.790113296761382 1.4402795782347964 chr4 191154276 162500894 0.8501033688621227 1.4913611971275433 chr5 180915260 140828082 0.7784201399041739 1.3940247602742544 chr6 171115067 97448657 0.5694919723229281 1.2363903691902698 chr7 159138663 164752126 1.0352740364546107 3.3950280202405403 chr8 146364022 159495744 1.0897196033599021 1.7948232400076203 chr9 141213431 71360261 0.5053362169211794 1.2677760952471282 chr10 135534747 32770091 0.24178368813423173 1.7156999274434914 chr11 135006516 90691823 0.6717588579206059 1.3338222044172077 chr12 133851895 93225320 0.6964811368565234 1.448617615494992 chr13 115169878 69587683 0.6042177365161401 1.2623264384403092 chr14 107349540 61219178 0.5702789038499839 1.2290135892480392 chr15 102531392 44179010 0.430882768079458 1.1070686945782793 chr16 90354753 34275198 0.3793402877212226 1.0094254634215587 chr17 81195210 29322508 0.36113593400398863 0.9999812964056172 chr18 78077248 49051492 0.6282430958632148 1.2288299607274458 chr19 59128983 18698399 0.3162306884256744 1.0805608273417273 chr20 63025520 32311369 0.5126712004914834 1.2707858897746445 chr21 48129895 22972506 0.47730222557103025 1.12519479033263 chr22 51304566 9907982 0.19312086179619958 0.6883477627205057 chrMT 16571 1215 0.07332086174642448 0.31537822729572246 chrX 155270560 149659500 0.9638626923223566 1.8026133123234498 chrY 59373566 1422644 0.02396089869353645 0.3685069979933038