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
A2 F1 I0 R1	4577	57.4	3436498	77.7%	2670158	63.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	646,754	G→A	22.6%	S101F (TCC→TTC)	pncB ←	nicotinate phosphoribosyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	646,754	0	G	A	22.6%	89.5 / 17.9	66	S101F (TCC→TTC)	pncB	nicotinate phosphoribosyltransferase
Reads supporting (aligned to +/- strand): ref base G (26/25); new base A (10/5); total (36/30)
Fisher's exact test for biased strand distribution p-value = 3.80e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.10e-01

AACTTCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGATAGTCG  >  minE/646687‑646810

aaCTTCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGa                                                         <  1:2489079/69‑1 (MQ=255)

aaCTTCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGa                                                         <  1:234247/69‑1 (MQ=255)

aaCTTCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGa                                                         <  1:1796635/69‑1 (MQ=255)

aaCTTCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGa                                                         <  1:1800696/69‑1 (MQ=255)

aaCTTCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGa                                                         <  1:2832304/69‑1 (MQ=255)

aaCTTCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGa                                                         <  1:1867450/69‑1 (MQ=255)

aaCTTCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGa                                                         <  1:3142783/69‑1 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCTATTATCGTTGAac                                                        >  1:3352448/1‑66 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        >  1:1159223/1‑66 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        <  1:2670653/66‑1 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        >  1:2739165/1‑66 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        >  1:2739562/1‑66 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        <  1:2423391/66‑1 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        <  1:2969337/66‑1 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        <  1:3101614/66‑1 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        >  1:3229277/1‑66 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        >  1:34966/1‑66 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        >  1:1992288/1‑66 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        >  1:38913/1‑66 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        <  1:1192386/66‑1 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        >  1:2043509/1‑66 (MQ=255)

    tCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGAac                                                        >  1:749674/1‑66 (MQ=255)

                    cACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCggg                                      >  1:1728396/1‑68 (MQ=255)

                    cACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCggg                                      >  1:2487483/1‑68 (MQ=255)

                    cACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCggg                                      >  1:1846369/1‑68 (MQ=255)

                    cACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCggg                                      >  1:3032007/1‑68 (MQ=255)

                    cACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTGCCggg                                      >  1:229597/1‑68 (MQ=255)

                            gggCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGa                                                         <  1:2660698/41‑1 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             >  1:695411/1‑61 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             >  1:789639/1‑61 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             >  1:932737/1‑61 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             >  1:99643/1‑61 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             >  1:2661465/1‑61 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             >  1:2657440/1‑61 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             >  1:2017150/1‑61 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             <  1:2571261/61‑1 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             >  1:1446095/1‑61 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             >  1:1551349/1‑61 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             >  1:2093595/1‑61 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             >  1:1991042/1‑61 (MQ=255)

                                    tAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCgg                             >  1:2245786/1‑61 (MQ=255)

                                                cAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTaa          >  1:2580363/1‑68 (MQ=255)

                                                cAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTaa          >  1:2079161/1‑68 (MQ=255)

                                                cAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTaa          >  1:3313095/1‑68 (MQ=255)

                                                cAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTaa          >  1:2094552/1‑68 (MQ=255)

                                                cAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTaa          >  1:3106560/1‑68 (MQ=255)

                                                cAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTaa          >  1:689318/1‑68 (MQ=255)

                                                cAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTaa          >  1:2916989/1‑68 (MQ=255)

                                                cAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTaa          >  1:225213/1‑68 (MQ=255)

                                                cAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTaa          >  1:78243/1‑68 (MQ=255)

                                                  gCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGAt       <  1:1833301/69‑1 (MQ=255)

                                                  gCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGAt       <  1:175833/69‑1 (MQ=255)

                                                  gCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGAt       <  1:412876/69‑1 (MQ=255)

                                                  gCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGAt       <  1:261428/69‑1 (MQ=255)

                                                  gCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGAt       <  1:1143931/69‑1 (MQ=255)

                                                  gCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGAt       <  1:3166570/69‑1 (MQ=255)

                                                  gCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGAt       <  1:2096557/69‑1 (MQ=255)

                                                  gCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGAt       <  1:2507137/69‑1 (MQ=255)

                                                  gCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGAt       <  1:2558926/69‑1 (MQ=255)

                                                   cTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGATa      <  1:685449/69‑1 (MQ=255)

                                                   cTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGATa      <  1:3083368/69‑1 (MQ=255)

                                                   cTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGATa      <  1:2791228/69‑1 (MQ=255)

                                                   cTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGATa      <  1:2425560/69‑1 (MQ=255)

                                                   cTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGATa      <  1:914699/69‑1 (MQ=255)

                                                        cATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGATAGTCg  <  1:2105767/68‑1 (MQ=255)

                                                              cGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGAt       <  1:318898/57‑1 (MQ=255)

AACTTCCCAGAGGATGACTTCACGCCACGGGCCGCTTAAACGAATATCCAGCTTGCCATTATCGTTGGACACGGTGACTTGTTCCGGGTTAAAGCGGAACTCGCGTAACCAGTTAAGATAGTCG  >  minE/646687‑646810

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A