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	749,189	T→A	33.7%	S147S (TCA→TCT)	ycfS ←	conserved hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	749,189	0	T	A	33.7%	90.0 / 71.1	92	S147S (TCA→TCT)	ycfS	conserved hypothetical protein
Reads supporting (aligned to +/- strand): ref base T (20/41); new base A (24/7); total (44/48)
Fisher's exact test for biased strand distribution p-value = 6.10e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.05e-01

TCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATACC  >  minE/749123‑749245

tCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGa                                                        >  1:345786/1‑69 (MQ=255)

tCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGa                                                        >  1:552075/1‑69 (MQ=255)

tCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGa                                                        >  1:2692866/1‑69 (MQ=255)

tCCCTGTGCCTTATACCGCGCGCGAATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGCTTGTCAGa                                                        <  1:2674091/69‑1 (MQ=25)

tCCCTGTGCCTTATACCGCGCGCGAATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGCTTGTCAGa                                                        <  1:2176335/69‑1 (MQ=25)

tCCCTGTGCCTTATACCGCGCGCGAATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGCTTGTCAGa                                                        <  1:2942480/69‑1 (MQ=25)

tCCCTGTGCCTTATACCGCGCGCGAATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGCTTGTCAGa                                                        <  1:2678143/69‑1 (MQ=25)

tCCCTGTGCCTTATACCGCGCGCGAATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGCTTGTCAGa                                                        <  1:1302466/69‑1 (MQ=25)

tCCCTGTGCCTTATACCGCGCGCGAATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGCTTGTCAGa                                                        <  1:1205985/69‑1 (MQ=25)

tCCCTGTGCCTTATACCGCGCGCGAATGTTTGCCGTTGGCGTACAGGTTGGGTTTGCACGCTTGTCAGa                                                        <  1:1173620/69‑1 (MQ=25)

        cTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACggtg                                                 >  1:3081829/1‑68 (MQ=255)

        cTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACggtg                                                 >  1:2366282/1‑68 (MQ=255)

                      cgGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGgt                                  <  1:3185877/69‑1 (MQ=255)

                        gATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGgt                                  >  1:710605/1‑67 (MQ=255)

                        gATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGgt                                  >  1:3292180/1‑67 (MQ=255)

                                 cGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCgtgt                        <  1:3346449/68‑1 (MQ=255)

                                 cGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCgtgt                        <  1:220712/68‑1 (MQ=255)

                                 cGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCgtgt                        <  1:196441/68‑1 (MQ=255)

                                 cGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCgtgt                        <  1:3251937/68‑1 (MQ=255)

                                 cGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCgtgt                        <  1:996869/68‑1 (MQ=255)

                                 cGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCgtgt                        <  1:43/68‑1 (MQ=255)

                                   ttGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTcac                     <  1:1612913/69‑1 (MQ=255)

                                   ttGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTcac                     <  1:2930998/69‑1 (MQ=255)

                                   ttGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTcac                     <  1:173787/69‑1 (MQ=255)

                                   ttGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTcac                     <  1:2649570/69‑1 (MQ=255)

                                        gTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCt                <  1:2857212/69‑1 (MQ=255)

                                        gTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCt                <  1:759264/69‑1 (MQ=255)

                                        gTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCt                <  1:2039040/69‑1 (MQ=255)

                                        gTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCt                <  1:1444728/69‑1 (MQ=255)

                                        gTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCt                <  1:1987758/69‑1 (MQ=255)

                                        gTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCt                <  1:612521/69‑1 (MQ=255)

                                        gTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCt                <  1:1470657/69‑1 (MQ=255)

                                        gTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCt                <  1:1505377/69‑1 (MQ=255)

                                        gTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCt                <  1:3262651/69‑1 (MQ=255)

                                        gTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCt                <  1:1551507/69‑1 (MQ=255)

                                        gTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCt                <  1:2396275/69‑1 (MQ=255)

                                        gTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCt                <  1:128267/69‑1 (MQ=255)

                                         tCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTa               <  1:1682385/69‑1 (MQ=255)

                                         tCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTa               <  1:3001672/69‑1 (MQ=255)

                                         tCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTa               <  1:1605395/69‑1 (MQ=255)

                                         tCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTa               <  1:14252/69‑1 (MQ=255)

                                         tCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTa               <  1:1146038/69‑1 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGc                            >  1:1048503/1‑54 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           >  1:3033925/1‑55 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           <  1:3252285/55‑1 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           >  1:2521627/1‑55 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           <  1:3337798/55‑1 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           >  1:3357920/1‑55 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           >  1:654937/1‑55 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           <  1:2676037/55‑1 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           >  1:837180/1‑55 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           >  1:2558493/1‑55 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           <  1:2579487/55‑1 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           >  1:1632688/1‑55 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           >  1:1688717/1‑55 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           >  1:2422920/1‑55 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           <  1:2409645/55‑1 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           >  1:2335344/1‑55 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           >  1:2077775/1‑55 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           >  1:120005/1‑55 (MQ=255)

                                           cAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGGCGGTGTCAGCg                           <  1:1275800/55‑1 (MQ=255)

                                                tGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGAcc        <  1:3347976/69‑1 (MQ=255)

                                                tGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGAcc        <  1:1456805/69‑1 (MQ=255)

                                                tGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGAcc        <  1:888636/69‑1 (MQ=255)

                                                   gTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCg                           <  1:249408/47‑1 (MQ=255)

                                                    tttGCAGGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:393638/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCa       >  1:1924756/1‑66 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:1259560/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:955012/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:1522990/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:152635/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:413442/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:1623411/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:1191642/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:1623917/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:998062/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:1658697/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:3284956/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:1757277/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:3200444/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:1951992/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:2014453/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:3072477/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:2974891/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:2700531/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAtg    >  1:2685144/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAt     >  1:191381/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAt     >  1:311914/1‑68 (MQ=255)

                                                    tttGCACGCTTGTCAGAAACAGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAAt     >  1:2191323/1‑68 (MQ=255)

                                                      tGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATAcc  <  1:1381902/69‑1 (MQ=255)

                                                      tGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATAcc  <  1:782459/69‑1 (MQ=255)

                                                      tGCACGTTTGTCTGAAACGGTGGTCACCATTGACGGTGTCAGCGTGTCACCACCTAACTGACCAATAcc  <  1:3091965/69‑1 (MQ=255)

TCCCTGTGCTTTATAACGGGCGCGGATGTTTGCCGTTGGCGTCCAGGTTGGGTTTGCACGTTTGTCTGAAACGGTGGTCACCATTGTCGGTGTCAGCGTGTCACCACCTAACTGACCAATACC  >  minE/749123‑749245

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 21 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A