BamQC report ----------------------------------- >>>>>>> Input bam file = ERR9714158.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 809,978 number of mapped reads = 543,765 (67.13%) number of supplementary alignments = 16,181 (2%) number of secondary alignments = 0 number of mapped bases = 70,862,781 bp number of sequenced bases = 69,249,143 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 484,297 duplication rate = 44% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.8738 >>>>>>> ACTG content number of A's = 18,540,607 bp (26.77%) number of C's = 15,503,391 bp (22.39%) number of T's = 17,565,530 bp (25.37%) number of G's = 17,639,045 bp (25.47%) number of N's = 570 bp (0%) GC percentage = 47.86% >>>>>>> Mismatches and indels general error rate = 0.0444 number of mismatches = 2,874,111 number of insertions = 73,601 mapped reads with insertion percentage = 13.04% number of deletions = 256,181 mapped reads with deletion percentage = 44.71% homopolymer indels = 30.44% >>>>>>> Coverage mean coverageData = 0.0229X std coverageData = 5.9658X There is a 0.06% of reference with a coverageData >= 1X There is a 0.04% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.03% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% 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 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 6391830 0.02564418886643416 7.410540109172132 chr2 243199373 8624295 0.03546183073424289 10.236075429506117 chr3 198022430 2305906 0.01164467075775204 2.3934743399123435 chr4 191154276 2023063 0.010583404370195726 2.1644319104994785 chr5 180915260 3274949 0.01810211587458128 3.352296099064357 chr6 171115067 2707358 0.015821856295097615 3.32193195428944 chr7 159138663 2080484 0.01307340379000168 2.124036972222428 chr8 146364022 2600942 0.01777036435907726 3.7003601167090174 chr9 141213431 2722170 0.019276990727602958 4.104052722531184 chr10 135534747 3285052 0.02423771079160977 3.6640230768375264 chr11 135006516 2990378 0.022149879047319465 3.2065482573935444 chr12 133851895 4365922 0.03261755838421264 7.694009500266003 chr13 115169878 2828507 0.024559433847798292 8.200876510556373 chr14 107349540 3871106 0.036060760018161234 16.24477825986302 chr15 102531392 2444214 0.023838689325509206 3.920683348446877 chr16 90354753 1184805 0.013112813224114507 1.7296931428331301 chr17 81195210 2824121 0.034781867058413914 6.182637360646128 chr18 78077248 2160317 0.027668969582534467 5.3072744088359425 chr19 59128983 2039199 0.03448730041577072 3.7859367594328748 chr20 63025520 2301700 0.036520127085028414 5.349935175145582 chr21 48129895 761207 0.015815679631131545 2.8749542563967827 chr22 51304566 541385 0.01055237461710523 1.290404521437593 chrMT 16571 92393 5.575583851306499 44.54293930950451 chrX 155270560 5794566 0.03731915438444996 3.6619221447493353 chrY 59373566 646912 0.010895623146502604 2.4314338149327734