BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013322.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 = 1,657,640 number of mapped reads = 1,176,274 (70.96%) number of supplementary alignments = 6,392 (0.39%) number of secondary alignments = 0 number of mapped bases = 71,003,747 bp number of sequenced bases = 70,973,031 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 59,465 duplication rate = 4.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7335 >>>>>>> ACTG content number of A's = 20,378,570 bp (28.71%) number of C's = 11,964,282 bp (16.86%) number of T's = 21,938,066 bp (30.91%) number of G's = 16,667,479 bp (23.48%) number of N's = 24,634 bp (0.03%) GC percentage = 40.34% >>>>>>> Mismatches and indels general error rate = 0.0112 number of mismatches = 787,359 number of insertions = 4,625 mapped reads with insertion percentage = 0.39% number of deletions = 18,771 mapped reads with deletion percentage = 1.58% homopolymer indels = 48.04% >>>>>>> Coverage mean coverageData = 0.0229X std coverageData = 0.1998X There is a 1.93% of reference with a coverageData >= 1X There is a 0.28% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 5596668 0.022453978158794637 0.24638813454385206 chr2 243199373 8651475 0.03557359089079559 0.23993884949044167 chr3 198022430 4493314 0.022690934557262024 0.17451279548929072 chr4 191154276 4509337 0.023590039911008845 0.18243196366360867 chr5 180915260 3468776 0.01917348486799842 0.1618143694658467 chr6 171115067 3382780 0.019769036469477 0.1786628762463406 chr7 159138663 4343689 0.027294994931558524 0.2854001058314612 chr8 146364022 4242824 0.028988162131811327 0.2514558829463883 chr9 141213431 2540526 0.01799068248685212 0.17160287682461384 chr10 135534747 3229618 0.023828708663174027 0.1941832708831274 chr11 135006516 3118879 0.023101692365722556 0.19466945523125162 chr12 133851895 3739190 0.027935278764637587 0.1962076068003097 chr13 115169878 1434835 0.012458422505231794 0.128607006885422 chr14 107349540 2532996 0.023595778798865836 0.1810034672655371 chr15 102531392 2062068 0.020111577145075724 0.17598285272670317 chr16 90354753 2117665 0.02343722858718899 0.1805195514690315 chr17 81195210 1570106 0.0193374215055297 0.1677702876243967 chr18 78077248 1539086 0.019712349492646053 0.22040546740791214 chr19 59128983 1157718 0.01957953513254236 0.19063050163400624 chr20 63025520 1530909 0.024290303356481628 0.1821213609989202 chr21 48129895 1366232 0.028386349066417037 0.20113643170292947 chr22 51304566 578166 0.011269289365005056 0.12068110561987888 chrMT 16571 11760 0.7096735260394665 1.0764157818012798 chrX 155270560 3648443 0.023497326215607132 0.1844616767574163 chrY 59373566 136687 0.0023021524427217326 0.055650052626379204