BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1779169.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 = 68,290,020 number of mapped reads = 66,036,114 (96.7%) number of supplementary alignments = 366,089 (0.54%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 33,357,074 number of mapped paired reads (second in pair) = 32,679,040 number of mapped paired reads (both in pair) = 65,115,976 number of mapped paired reads (singletons) = 920,138 number of mapped bases = 6,598,965,307 bp number of sequenced bases = 6,597,508,853 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,747,136 duplication rate = 4.96% >>>>>>> Insert size mean insert size = 63,627.3249 std insert size = 2,441,255.0589 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 53.4683 >>>>>>> ACTG content number of A's = 2,014,886,640 bp (30.54%) number of C's = 1,277,105,200 bp (19.36%) number of T's = 2,009,104,020 bp (30.45%) number of G's = 1,293,749,130 bp (19.61%) number of N's = 2,663,863 bp (0.04%) GC percentage = 38.97% >>>>>>> Mismatches and indels general error rate = 0.0043 number of mismatches = 27,061,681 number of insertions = 539,666 mapped reads with insertion percentage = 0.81% number of deletions = 650,538 mapped reads with deletion percentage = 0.97% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 2.1317X std coverageData = 4.94X There is a 51.82% of reference with a coverageData >= 1X There is a 36.15% of reference with a coverageData >= 2X There is a 26.05% of reference with a coverageData >= 3X There is a 19.37% of reference with a coverageData >= 4X There is a 14.7% of reference with a coverageData >= 5X There is a 11.34% of reference with a coverageData >= 6X There is a 8.88% of reference with a coverageData >= 7X There is a 7.04% of reference with a coverageData >= 8X There is a 5.64% of reference with a coverageData >= 9X There is a 4.57% of reference with a coverageData >= 10X There is a 3.73% of reference with a coverageData >= 11X There is a 3.07% of reference with a coverageData >= 12X There is a 2.55% of reference with a coverageData >= 13X There is a 2.13% of reference with a coverageData >= 14X There is a 1.79% of reference with a coverageData >= 15X There is a 1.51% of reference with a coverageData >= 16X There is a 1.28% of reference with a coverageData >= 17X There is a 1.1% of reference with a coverageData >= 18X There is a 0.94% of reference with a coverageData >= 19X There is a 0.81% of reference with a coverageData >= 20X There is a 0.7% of reference with a coverageData >= 21X There is a 0.61% of reference with a coverageData >= 22X There is a 0.53% of reference with a coverageData >= 23X There is a 0.47% of reference with a coverageData >= 24X There is a 0.41% of reference with a coverageData >= 25X There is a 0.36% of reference with a coverageData >= 26X There is a 0.32% of reference with a coverageData >= 27X There is a 0.29% of reference with a coverageData >= 28X There is a 0.26% of reference with a coverageData >= 29X There is a 0.23% of reference with a coverageData >= 30X There is a 0.21% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.17% of reference with a coverageData >= 33X There is a 0.15% of reference with a coverageData >= 34X There is a 0.14% of reference with a coverageData >= 35X There is a 0.13% of reference with a coverageData >= 36X There is a 0.12% of reference with a coverageData >= 37X There is a 0.11% of reference with a coverageData >= 38X There is a 0.1% of reference with a coverageData >= 39X There is a 0.09% of reference with a coverageData >= 40X There is a 0.08% of reference with a coverageData >= 41X There is a 0.08% of reference with a coverageData >= 42X There is a 0.07% of reference with a coverageData >= 43X There is a 0.07% of reference with a coverageData >= 44X There is a 0.06% of reference with a coverageData >= 45X There is a 0.06% of reference with a coverageData >= 46X There is a 0.06% of reference with a coverageData >= 47X There is a 0.05% of reference with a coverageData >= 48X There is a 0.05% of reference with a coverageData >= 49X There is a 0.05% of reference with a coverageData >= 50X There is a 0.05% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 514773054 2.0652829346411137 4.670349296082024 chr2 243199373 575480548 2.366291248620941 4.7943830075151554 chr3 198022430 479390319 2.4208889821218738 4.142548487445999 chr4 191154276 518338143 2.7116220146704957 4.47802539102013 chr5 180915260 370193399 2.046225393037602 3.637971734142281 chr6 171115067 395528468 2.311476569155655 3.9586042440741385 chr7 159138663 563631333 3.541762400002066 11.675650634590852 chr8 146364022 543682418 3.7145905842899016 5.318247273668499 chr9 141213431 242263639 1.7155849644358545 3.6785435326064433 chr10 135534747 114334803 0.8435829595786237 6.39452336495221 chr11 135006516 287224354 2.127485120792244 3.7956314147804604 chr12 133851895 310808539 2.322033162100544 4.231206675099191 chr13 115169878 195272609 1.6955180676669641 3.3823511924873877 chr14 107349540 209217461 1.9489367257651966 3.767549656592142 chr15 102531392 111804597 1.090442593425436 2.9626297023818364 chr16 90354753 84416547 0.9342789858547895 2.2981946546164504 chr17 81195210 112790816 1.3891314031948436 3.2008934094912416 chr18 78077248 186019845 2.382510267267617 3.900540990616484 chr19 59128983 64677222 1.0938328163026243 2.9865466005599526 chr20 63025520 149461117 2.371438061915237 4.251252861105797 chr21 48129895 74273509 1.5431886772244152 3.0861310576289425 chr22 51304566 40171835 0.783007013449836 2.1496091727493223 chrMT 16571 4639 0.27994689517832355 0.7097638936206839 chrX 155270560 450507242 2.9014337424943917 5.101216284012199 chrY 59373566 4698851 0.07914045452483012 1.0836833224154698