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
A19 F42 I1 R1	11	27.7	610674	93.3%	569758	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,034,506	T→C	H68R (CAT→CGT)	murE2 ←	UDP‑N‑acetylmuramoylalanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,034,506	0	T	C	95.7%	76.5 / NA	23	H68R (CAT→CGT)	murE2	UDP‑N‑acetylmuramoylalanyl‑D‑glutamate‑‑2, 6‑diaminopimelate ligase
Reads supporting (aligned to +/- strand): ref base T (0/0); major base C (9/13); minor base G (1/0); total (10/13)
Fisher's exact test for biased strand distribution p-value = 4.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCTTCATCAATTTCGATTACCGCAATTTTAGTCTTAGGTGTTGATTGCATGATGAATGCAGAAGTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTATGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGCTCTGCTAATTTTCTTAATATATCTGTATCCACTTTTCTAGCGATTTGTCC  >  CP000730/2034373‑2034624

aCCTTCATCAATTTCGATTACCGCAATTTTAGTCTTAGGTGTTGATTGCATGATGAATGCAGAAGTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAAt                                                                                                                 >  1:222646/1‑141 (MQ=255)

  cTTCATCAATTTCGATTACCGCAATTTTAGTCTTAGGTGTTGATTGCATGATGAATGCAGAAGTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTa                                                                                                               >  2:1963/1‑141 (MQ=255)

    tcatcaATTTCGATTACCGCAATTTTAGTCTTAGGTGTTGATTGCATGATGAATGCAGAAGTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAg                                                                                                             >  2:284368/1‑141 (MQ=255)

        caATTTCGATTACCGCAATTTTAGTCTTAGGTGTTGATTGCATGATGAATGTAGAAGTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTg                                                                                                         <  2:208087/141‑1 (MQ=255)

                    ccGCAATTTTAGTCTTAGGTGTTGATTGCATGATGAATGCAGAAGTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGttt                                                                                             >  1:2505/1‑141 (MQ=255)

                                             ttGCATGATGAATGCAGAAGTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATAc                                                                    <  2:76784/141‑1 (MQ=255)

                                             ttGCATGATGAATGCAGAAGTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCAGTTGTTCCACTGATAAATAc                                                                    <  2:28053/141‑1 (MQ=255)

                                                         tGCAGAAGTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAAc                                                        <  1:102455/141‑1 (MQ=255)

                                                         tGCAGAAGTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAAc                                                        <  1:303910/141‑1 (MQ=255)

                                                            aGAAGTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTg                                                     >  1:82029/1‑141 (MQ=255)

                                                              aatgtttaCCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGct                                                   <  1:39/135‑1 (MQ=255)

                                                                gTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTCGGTCCTATTAAGACGGTAGTCGGTGTTGTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGctct                                                 >  1:212442/1‑141 (MQ=255)

                                                                gTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTCCGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGctct                                                 >  1:111771/1‑141 (MQ=255)

                                                                gTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGctct                                                 <  1:201335/141‑1 (MQ=255)

                                                                  tataCCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGCTCTGc                                               <  2:243242/141‑1 (MQ=255)

                                                                                    aGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGCTCTGCTAATTTTCTTAATATATc                             <  1:199906/141‑1 (MQ=255)

                                                                                           tCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGCTCTGCTAATTTTCTTAATATATCTGTATcc                      >  2:83020/1‑141 (MQ=255)

                                                                                           tCATTATTGTGTATAATGTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGCTCTGCTAATTTTCTTAATATATCTGTATcc                      <  2:273330/141‑1 (MQ=255)

                                                                                             attattGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGCTCTGCTAATTTTCTTAATATATCTGTATCCAc                    <  1:129223/141‑1 (MQ=255)

                                                                                             attattGTGTATAATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGCTCTGCTAATTTTCTTAATATATCTGTATCCAc                    <  2:305034/141‑1 (MQ=255)

                                                                                                      tataATTTGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGCTCTGCTAATTTTCTTAATATATCTGTATCCACTTTTCTAGc           <  1:295500/141‑1 (MQ=255)

                                                                                                             tGAATATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAGTATCATCAACTTGCTCTGCTAATTTTCTTAATATATCTGTATCCACTTTTCTAGCGATTTGt    >  2:161631/1‑141 (MQ=255)

                                                                                                               aaTATTATTTGCTTTTAAAGTACGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGCTCTGCTAATTTTCTTAATATATCTGTATCCACTTTTCTAGCGATTTGTcc  >  1:234547/1‑141 (MQ=255)

ACCTTCATCAATTTCGATTACCGCAATTTTAGTCTTAGGTGTTGATTGCATGATGAATGCAGAAGTTATACCTGCAGCCATATTAGCACCTTCATTATTGTGTATAATTTGAATATTATTTGCTTTTAAAGTATGTCCAATTAAGTTTGAAGTCGTTGTTTTACCATTTGTTCCACTGATAAATACAATATCATCAACTTGCTCTGCTAATTTTCTTAATATATCTGTATCCACTTTTCTAGCGATTTGTCC  >  CP000730/2034373‑2034624

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A