BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6237843.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 = 2,336,057
number of mapped reads = 1,966,570 (84.18%)
number of supplementary alignments = 10,789 (0.46%)
number of secondary alignments = 0
number of mapped bases = 124,695,699 bp
number of sequenced bases = 124,641,553 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 93,328
duplication rate = 3.53%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.1362
>>>>>>> ACTG content
number of A's = 34,211,841 bp (27.45%)
number of C's = 22,233,774 bp (17.84%)
number of T's = 40,075,340 bp (32.15%)
number of G's = 28,008,516 bp (22.47%)
number of N's = 112,082 bp (0.09%)
GC percentage = 40.31%
>>>>>>> Mismatches and indels
general error rate = 0.0083
number of mismatches = 1,014,092
number of insertions = 11,244
mapped reads with insertion percentage = 0.57%
number of deletions = 32,788
mapped reads with deletion percentage = 1.65%
homopolymer indels = 47.27%
>>>>>>> Coverage
mean coverageData = 0.0403X
std coverageData = 0.3927X
There is a 3.38% of reference with a coverageData >= 1X
There is a 0.45% of reference with a coverageData >= 2X
There is a 0.08% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% 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 6990094 0.028044439656581637 0.49395100748411597
chr2 243199373 8110492 0.03334914847827342 0.4188625307164404
chr3 198022430 16286856 0.082247531251889 0.33079779746090865
chr4 191154276 4636408 0.02425479616265555 0.23331303055114364
chr5 180915260 5990202 0.03311054026067232 0.21185929193256658
chr6 171115067 5249377 0.030677468045522842 0.2202170560814304
chr7 159138663 10543471 0.06625335918525344 0.8112210884084093
chr8 146364022 5140670 0.03512249752196615 0.38948205220345916
chr9 141213431 5520936 0.039096394449901865 0.44726034818825977
chr10 135534747 6000182 0.044270433470466435 0.43317093055220013
chr11 135006516 7705758 0.05707693397554234 0.37749319818836014
chr12 133851895 7264671 0.054273949576881225 0.2822287294312497
chr13 115169878 6873223 0.05967899870485232 0.2799353914252212
chr14 107349540 4364974 0.04066132002056087 0.29249889668158596
chr15 102531392 1716072 0.01673703991066463 0.14951995488726924
chr16 90354753 2283486 0.02527245024951814 0.2577020048048051
chr17 81195210 2778453 0.03421942008648047 0.2623350690701507
chr18 78077248 2976585 0.03812359011424173 0.7897308678675418
chr19 59128983 2281357 0.03858272008500468 0.39671903547315657
chr20 63025520 2513264 0.03987692604519566 0.2554965067254973
chr21 48129895 2054707 0.0426908681184532 0.29008398917709155
chr22 51304566 1835210 0.03577089025565483 0.21623392593065915
chrMT 16571 88940 5.367207772614809 4.173681289059653
chrX 155270560 5116073 0.032949407795012785 0.2626106082241918
chrY 59373566 374238 0.006303108019484631 0.18062910263120496