level 1
真暖越n
楼主
150bp 的情况下
Left reads:
Input : 40496330
Mapped : 17652570 (43.6% of input)
of these: 872758 ( 4.9%) have multiple alignments(5909 have >20)
Right reads:
Input : 40496330
Mapped : 16094620 (39.7% of input)
of these: 885334 ( 5.5%) have multiple alignments(5830 have >20)
41.7% overallread mapping rate.
Alignedpairs: 15240029
of these: 723221 ( 4.7%) have multiple alignments
60298 ( 0.4%) are discordantalignments
37.5% concordantpair alignment rate.
随后对这150bp截短，右端去掉50bp，只剩100bp
Left reads:
Input : 40496330
Mapped : 26896059 (66.4% of input)
of these: 1524759 ( 5.7%) have multiple alignments(15603 have >20)
Right reads:
Input : 40496330
Mapped : 25305528 (62.5% of input)
of these: 1437492 ( 5.7%) have multiple alignments(15475 have >20)
64.5% overall read mapping rate.
Aligned pairs: 24389919
of these: 1377238 ( 5.6%) have multiplealignments
243745 ( 1.0%) arediscordant alignments
59.6% concordant pair alignment rate.
alignment-rate前后竟然差了20%！请问这是怎么回事。我随后用其他数据跑了发现150bp的大多都在40%左右，100bp的大多在60%左右。
2015年10月19日 05点10分
1
Left reads:
Input : 40496330
Mapped : 17652570 (43.6% of input)
of these: 872758 ( 4.9%) have multiple alignments(5909 have >20)
Right reads:
Input : 40496330
Mapped : 16094620 (39.7% of input)
of these: 885334 ( 5.5%) have multiple alignments(5830 have >20)
41.7% overallread mapping rate.
Alignedpairs: 15240029
of these: 723221 ( 4.7%) have multiple alignments
60298 ( 0.4%) are discordantalignments
37.5% concordantpair alignment rate.
随后对这150bp截短，右端去掉50bp，只剩100bp
Left reads:
Input : 40496330
Mapped : 26896059 (66.4% of input)
of these: 1524759 ( 5.7%) have multiple alignments(15603 have >20)
Right reads:
Input : 40496330
Mapped : 25305528 (62.5% of input)
of these: 1437492 ( 5.7%) have multiple alignments(15475 have >20)
64.5% overall read mapping rate.
Aligned pairs: 24389919
of these: 1377238 ( 5.6%) have multiplealignments
243745 ( 1.0%) arediscordant alignments
59.6% concordant pair alignment rate.
alignment-rate前后竟然差了20%！请问这是怎么回事。我随后用其他数据跑了发现150bp的大多都在40%左右，100bp的大多在60%左右。
