BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1781813.sorted.bam outfile = /home/yangyx/scDNA/SRP052954/SRP052954.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 = 300,643,564 number of mapped reads = 287,133,113 (95.51%) number of supplementary alignments = 1,097,182 (0.36%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 147,321,228 number of mapped paired reads (second in pair) = 139,811,885 number of mapped paired reads (both in pair) = 278,181,586 number of mapped paired reads (singletons) = 8,951,527 number of mapped bases = 27,797,445,707 bp number of sequenced bases = 27,791,825,169 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 26,592,698 duplication rate = 8.87% >>>>>>> Insert size mean insert size = 45,782.4268 std insert size = 2,075,302.9448 median insert size = 211 >>>>>>> Mapping quality mean mapping quality = 53.733 >>>>>>> ACTG content number of A's = 8,123,548,045 bp (29.23%) number of C's = 5,707,939,016 bp (20.54%) number of T's = 8,080,527,029 bp (29.08%) number of G's = 5,795,411,892 bp (20.85%) number of N's = 84,399,187 bp (0.3%) GC percentage = 41.39% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 162,259,499 number of insertions = 2,510,019 mapped reads with insertion percentage = 0.86% number of deletions = 2,475,254 mapped reads with deletion percentage = 0.85% homopolymer indels = 45.66% >>>>>>> Coverage mean coverageData = 8.9794X std coverageData = 10.8317X There is a 88.99% of reference with a coverageData >= 1X There is a 84.71% of reference with a coverageData >= 2X There is a 79.12% of reference with a coverageData >= 3X There is a 72.69% of reference with a coverageData >= 4X There is a 65.89% of reference with a coverageData >= 5X There is a 59.09% of reference with a coverageData >= 6X There is a 52.56% of reference with a coverageData >= 7X There is a 46.47% of reference with a coverageData >= 8X There is a 40.9% of reference with a coverageData >= 9X There is a 35.89% of reference with a coverageData >= 10X There is a 31.43% of reference with a coverageData >= 11X There is a 27.5% of reference with a coverageData >= 12X There is a 24.05% of reference with a coverageData >= 13X There is a 21.03% of reference with a coverageData >= 14X There is a 18.41% of reference with a coverageData >= 15X There is a 16.13% of reference with a coverageData >= 16X There is a 14.14% of reference with a coverageData >= 17X There is a 12.42% of reference with a coverageData >= 18X There is a 10.92% of reference with a coverageData >= 19X There is a 9.61% of reference with a coverageData >= 20X There is a 8.48% of reference with a coverageData >= 21X There is a 7.49% of reference with a coverageData >= 22X There is a 6.63% of reference with a coverageData >= 23X There is a 5.88% of reference with a coverageData >= 24X There is a 5.22% of reference with a coverageData >= 25X There is a 4.65% of reference with a coverageData >= 26X There is a 4.14% of reference with a coverageData >= 27X There is a 3.69% of reference with a coverageData >= 28X There is a 3.3% of reference with a coverageData >= 29X There is a 2.96% of reference with a coverageData >= 30X There is a 2.65% of reference with a coverageData >= 31X There is a 2.38% of reference with a coverageData >= 32X There is a 2.14% of reference with a coverageData >= 33X There is a 1.93% of reference with a coverageData >= 34X There is a 1.74% of reference with a coverageData >= 35X There is a 1.58% of reference with a coverageData >= 36X There is a 1.43% of reference with a coverageData >= 37X There is a 1.3% of reference with a coverageData >= 38X There is a 1.18% of reference with a coverageData >= 39X There is a 1.07% of reference with a coverageData >= 40X There is a 0.98% of reference with a coverageData >= 41X There is a 0.89% of reference with a coverageData >= 42X There is a 0.81% of reference with a coverageData >= 43X There is a 0.74% of reference with a coverageData >= 44X There is a 0.68% of reference with a coverageData >= 45X There is a 0.62% of reference with a coverageData >= 46X There is a 0.57% of reference with a coverageData >= 47X There is a 0.53% of reference with a coverageData >= 48X There is a 0.49% of reference with a coverageData >= 49X There is a 0.45% of reference with a coverageData >= 50X There is a 0.41% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2210616626 8.869051628160236 15.990925070692109 chr2 243199373 2255349327 9.273664233501128 10.768606224621783 chr3 198022430 1897755099 9.583536062051152 8.210291270461658 chr4 191154276 1734884594 9.075834610155411 9.83009133213157 chr5 180915260 1663094068 9.192668810801257 7.8297023364733835 chr6 171115067 1602497516 9.365028714858873 9.381924918680031 chr7 159138663 1403671197 8.820428490089803 9.858054336118068 chr8 146364022 1381040145 9.435653148421952 8.437493423355187 chr9 141213431 1105514098 7.8286752908085635 10.800125667085789 chr10 135534747 1552349858 11.453519428490171 16.96644443350964 chr11 135006516 1269376813 9.402337387922817 8.776263405745226 chr12 133851895 1852649055 13.841037177695542 11.884255472551187 chr13 115169878 849079162 7.372406541925832 7.66779511250614 chr14 107349540 829189321 7.724200038491082 8.18035658923454 chr15 102531392 776191025 7.570276867010642 8.300786450646518 chr16 90354753 695075080 7.692733994856917 8.64471485086131 chr17 81195210 643945622 7.930832643945376 9.140253302229915 chr18 78077248 705720446 9.038746422005039 12.173619669991934 chr19 59128983 416381461 7.041918190948761 10.97828183299671 chr20 63025520 559214224 8.872822056843006 9.700275699300057 chr21 48129895 330880439 6.874738434397166 14.651031083003014 chr22 51304566 285414375 5.563137889130569 7.9307654091414905 chrMT 16571 3617105 218.2792227385191 53.665968235150764 chrX 155270560 1747296560 11.253237960885825 10.172110853745242 chrY 59373566 26642491 0.448726475347632 5.1917857053106395