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
A11 F50 I0 R1	804	34.5	1706502	92.5%	1578514	135.5

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	5,737,655	G→C	30.8%	intergenic (‑154/+48)	hutU ← / ← PP_5034	urocanate hydratase/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	5,737,655	0	G	C	30.8%	31.7 / 20.9	26	intergenic (‑154/+48)	hutU/PP_5034	urocanate hydratase/hypothetical protein
Reads supporting (aligned to +/- strand): ref base G (8/10); new base C (4/4); total (12/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.72e-01

TCCTCTGCGGTCGTCCGCGGGCGGGTATGTCGTGGTCAATATACAAACACACCTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGCCCCTGCACAACCAGCCCCAGCAATTCATCATTGCCTTCCAGCCGCAAGCAGTCGAACAACCCC  >  NC_002947/5737510‑5737799

tCCTCTGCGGTCGTCCGCGGGCGGGTATGTCGTGGTCAATATACAAACACACCTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCcgcccgcg                                                                                                                                              >  2:357427/1‑148 (MQ=255)

      gCGGTCGTCCGCGGGCGGGTATGTCGTGGTCAATATACAAACACACCTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCCCGCGCGgcgc                                                                                                                                        <  1:357427/150‑1 (MQ=255)

          tcgtcCGCGGGCGGGTATGTCGTGGTCAATATACAAACACACCTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGa                                                                                                                                    <  1:534635/150‑1 (MQ=255)

           cgtcCGCGGGCGGGTATGTCGTGGTCAATATACAAACACACCTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGAt                                                                                                                                   <  1:361481/150‑1 (MQ=255)

                 cgggcgggTATGTCGTGGTCAATATACAAACACACCTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTcaca                                                                                                                             <  1:699589/150‑1 (MQ=255)

                   ggcgggTATGTCGTGGTCAATATACAAACACACCTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTAGAGATCGAGCGCCGCCCGCGCGGCGCTCGAtctataccc                                                                                                                           <  1:752739/150‑7 (MQ=39)

                                   tCAATATACAAACACACCTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCCCGCGCGGCGCTCGa                                                                                                                                    >  1:553308/1‑125 (MQ=255)

                                   tCAATATACAAACACACCTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTCCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCCCGCGCGGCGCTCGa                                                                                                                                    <  2:553308/125‑1 (MQ=255)

                                                accccTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCCTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAgc                                                                                              <  1:97033/147‑1 (MQ=255)

                                                acacCTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGTGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAgc                                                                                              >  2:511724/1‑150 (MQ=255)

                                                  acCTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGTGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAgcgc                                                                                            <  1:511724/150‑1 (MQ=255)

                                                     tttACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCa                                                                                         >  1:621702/1‑150 (MQ=255)

                                                                 taCAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATc                                                                             >  1:473662/1‑150 (MQ=255)

                                                                                ccAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGcccc                                                              <  2:473662/150‑1 (MQ=255)

                                                                                 cAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGCCCCt                                                             >  1:722864/1‑150 (MQ=255)

                                                                                                         cTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGCCCCTGCACAACCAGCCCCAGCAATtcat                                     <  2:722864/150‑1 (MQ=255)

                                                                                                          tGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGCCCCTGCACAACCAGCCCCAGCAATtcatc                                    <  1:608854/150‑1 (MQ=255)

                                                                                                                   aTTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGCCCCt                                                             <  1:647315/116‑1 (MQ=255)

                                                                                                                   aTTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGCCCCt                                                             >  2:647315/1‑116 (MQ=255)

                                                                                                                                     aTCGAGCGCCGCGCGGGCGGCGCTCCATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCATCACCGCCCCTGCACAACCAGCCCCAGCAATTCATCATTGCCTTCCAGCCGCAAGCAGTCGaa         <  1:333867/150‑1 (MQ=255)

                                                                                                                                      tCGAGCGCCGCCCGCGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGCCCCTGCACAACCAGCCCCAGCAATTCATCATTGCCTTCCAGCCGCAAGCAGTCGaac        >  1:260004/1‑150 (MQ=255)

                                                                                                                                        gAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGCCCCTGCACAACCAGCCCCAGCAATTCATCATTGCCTTCCAGCCGCAAGCAGTCGaacaa      >  2:322049/1‑150 (MQ=255)

                                                                                                                                        gAGCGCCGCCCGCGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGccc                                                               <  1:559603/93‑1 (MQ=255)

                                                                                                                                        gAGCGCCGCCCGCGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGccc                                                               >  2:559603/1‑93 (MQ=255)

                                                                                                                                         aGCGCCGCCCGCGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGACAACACCGCCCCTGCACAACCATCCCCAGCAATTCATCATTGCCTTCCAGCCGCAAGCAGTCGaacaac     >  2:312372/1‑150 (MQ=39)

                                                                                                                                          gcgcCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGCCCCTGCACAACCAGCCCCAGCAATTCATCATTGCCTTCCAGCCGCAAGCAGTCGAACAAcc    >  2:336178/1‑150 (MQ=255)

                                                                                                                                            gccgcGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGCCCCTGCACAACCAGCCCCAGCAATTCATCATTGCCTTCCAGCCGCAAGCAGTCGAACAAcccc  >  2:455790/1‑150 (MQ=255)

TCCTCTGCGGTCGTCCGCGGGCGGGTATGTCGTGGTCAATATACAAACACACCTTTACTTGTATGTACAAGCATGGACAACCAAAATAATCGGACCTTACCGTTCCTGGCTTGAGATTTATGTTGGGGTATAGATCGAGCGCCGCGCGGGCGGCGCTCGATCTCACAGGCGCCAAAAATCTACAGCCGAACCTTCAGCGCCCATCAAGTTCGATCAGGCAGCACCGCCCCTGCACAACCAGCCCCAGCAATTCATCATTGCCTTCCAGCCGCAAGCAGTCGAACAACCCC  >  NC_002947/5737510‑5737799

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A