Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.

ALE, Flask, Isolate	Predicted Mutations	Mean Coverage	Total Reads	Percent Mapped	Mapped Reads	Average Read Length
A1 F2 I200 R1	216	30.8	1683622	97.2%	1636480	87.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NZ_CP009273	2,819,095	T→C	intergenic (‑160/‑96)	mltB ← / → srlA	lytic murein transglycosylase B/PTS glucitol/sorbitol transporter subunit IIC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NZ_CP009273	2,819,095	0	T	C	94.7%	53.4 / ‑3.7	19	intergenic (‑160/‑96)	mltB/srlA	lytic murein transglycosylase B/PTS glucitol/sorbitol transporter subunit IIC
Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (10/8); total (11/8)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATA  >  NZ_CP009273/2819012‑2819171

cTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCAtttt                                                                        >  2:235539/1‑90 (MQ=255)

    ccGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGa                                                                    <  1:613279/90‑1 (MQ=255)

      gATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATc                                                                  <  2:330866/90‑1 (MQ=255)

            gACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATa                                                            >  1:115905/1‑90 (MQ=255)

                ttACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAacac                                                        >  1:10031/1‑90 (MQ=255)

                          caactcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCt                                              >  2:685436/1‑90 (MQ=255)

                            actcaTTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCttt                                            >  1:713873/1‑90 (MQ=255)

                                 ttCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCGTTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc                                       <  1:693124/90‑1 (MQ=255)

                                 ttCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc                                       >  2:590009/1‑90 (MQ=255)

                                 ttCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc                                       >  1:306814/1‑90 (MQ=255)

                                 ttCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATc                                       >  2:835131/1‑90 (MQ=255)

                                     ccTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgat                                   <  1:426591/90‑1 (MQ=255)

                                      cTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgatt                                  <  2:306814/90‑1 (MQ=255)

                                      cTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTgatt                                  >  1:377124/1‑90 (MQ=255)

                                                    aTTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCg                    >  1:795494/1‑90 (MQ=255)

                                                      tCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGtt                  >  2:692800/1‑90 (MQ=255)

                                                        aaaCTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTg                <  1:647718/90‑1 (MQ=255)

                                                               cAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGtaataa         <  2:795494/90‑1 (MQ=255)

                                                                      aaaTATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATa  <  1:685436/90‑1 (MQ=255)

CTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATA  >  NZ_CP009273/2819012‑2819171

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

BRESEQ :: bam2aln output

AAGGAAGCGGTAGTCACTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAG  >  NZ_CP009273/2818996‑2819181

tctggttcgtgggctcggagatgtgtataagagacagTAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTC                                                                                        <  SRR3722079.215368/63‑1 (MQ=60)

                  GCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATA                                                                      >  SRR3722079.116859/1‑100 (MQ=60)

                    CCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAAC                                                                    <  SRR3722079.619494/100‑1 (MQ=60)

                      GATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACAC                                                                  >  SRR3722079.10109/1‑100 (MQ=60)

                                  ACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTT                                                      >  SRR3722079.721475/1‑100 (MQ=60)

                                       ACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATC                                                 >  SRR3722079.309306/1‑100 (MQ=60)

                                            ACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATT                                            >  SRR3722079.380184/1‑100 (MQ=60)

                                                 TTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCGTTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATT                                       <  SRR3722079.700416/100‑1 (MQ=60)

                                                     CCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGT                                   <  SRR3722079.430273/100‑1 (MQ=60)

                                                          CTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCG                              >  SRR3722079.804029/1‑100 (MQ=60)

                                                                        AAACTTTCAAATTAAAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAAC                <  SRR3722079.654411/100‑1 (MQ=60)

                                                                                      AAATATTTATCTTCCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAG  <  SRR3722079.692639/100‑1 (MQ=60)

AAGGAAGCGGTAGTCACTGCCCGATACGGACTTTACATAACTCAACTCATTCCCCTCGCTATCCTTTTATTCAAACTTTCAAATTAAAATATTTATCTTTCATTTTGCGATCAAAATAACACTTTTAAATCTTTCAATCTGATTAGATTAGGTTGCCGTTTGGTAATAAAACAATAAATCCTGAAG  >  NZ_CP009273/2818996‑2819181

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 0 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 35 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`