BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818788.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 767,140 number of mapped reads = 744,788 (97.09%) number of supplementary alignments = 5,672 (0.74%) number of secondary alignments = 0 number of mapped bases = 50,624,961 bp number of sequenced bases = 50,603,827 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 218,153 duplication rate = 26.41% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.739 >>>>>>> ACTG content number of A's = 14,195,319 bp (28.05%) number of C's = 10,831,449 bp (21.4%) number of T's = 14,663,166 bp (28.98%) number of G's = 10,910,890 bp (21.56%) number of N's = 3,003 bp (0.01%) GC percentage = 42.97% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 264,371 number of insertions = 6,428 mapped reads with insertion percentage = 0.85% number of deletions = 13,125 mapped reads with deletion percentage = 1.74% homopolymer indels = 38.52% >>>>>>> Coverage mean coverageData = 0.0164X std coverageData = 0.2357X There is a 1.04% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% 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 4181677 0.01677699731789234 0.2779614241980582 chr2 243199373 4443228 0.018269899075767766 0.38629017494411594 chr3 198022430 3533952 0.017846220753881266 0.19344708485559453 chr4 191154276 3233981 0.0169181724190151 0.20511460607325685 chr5 180915260 3147238 0.017396199745670984 0.20065291367447452 chr6 171115067 2961551 0.017307365458355574 0.20328693118715424 chr7 159138663 2778962 0.01746251946329347 0.21006021464787394 chr8 146364022 2640509 0.0180406971871817 0.209350686075421 chr9 141213431 2172692 0.0153858736000827 0.20124779762060155 chr10 135534747 2403834 0.0177359242054733 0.252367393944168 chr11 135006516 2426387 0.01797236957066576 0.2073054037465332 chr12 133851895 2344093 0.01751258732646258 0.19751736207544932 chr13 115169878 1612857 0.014004156538222607 0.17101713153845202 chr14 107349540 1571528 0.014639354765749346 0.19927767641723673 chr15 102531392 1459967 0.014239219535808116 0.17358405932184556 chr16 90354753 1533626 0.01697338489763787 0.2620336018870015 chr17 81195210 1337048 0.01646707976985342 0.19379274569301222 chr18 78077248 1363502 0.017463499738105525 0.2505415043673217 chr19 59128983 1010228 0.017085157713603836 0.2468285629113934 chr20 63025520 1095450 0.017381054531561184 0.20215767059433812 chr21 48129895 684315 0.01421808628504176 0.18065964629778355 chr22 51304566 635460 0.012386032073636487 0.17274048710899634 chrMT 16571 48391 2.9202220747088288 3.399803503930858 chrX 155270560 1560178 0.010048125027693595 0.1540865603801329 chrY 59373566 444307 0.007483245995364335 0.4018715404470563