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	2,904,683	T→C	29.5%	I471V (ATC→GTC)	treC ←	trehalose‑6‑P hydrolase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,904,683	0	T	C	29.5%	67.0 / 30.6	71	I471V (ATC→GTC)	treC	trehalose‑6‑P hydrolase
Reads supporting (aligned to +/- strand): ref base T (35/15); new base C (13/8); total (48/23)
Fisher's exact test for biased strand distribution p-value = 5.82e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.99e-01

CACGGCGATAGCACCACAATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAATCATCGGCCAGC  >  minE/2904617‑2904750

cACGGCTATAGCACCACAATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATgg                                                                   >  1:413604/1‑69 (MQ=255)

cACGGCGATAGCACCACAATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATgg                                                                   >  1:2032495/1‑69 (MQ=255)

cACGGCGATAGCACCACAATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATgg                                                                   >  1:3264414/1‑69 (MQ=255)

cACGGCGATAGCACCACAATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATgg                                                                   >  1:3292936/1‑69 (MQ=255)

cACGGCGATAGCACCACAATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATgg                                                                   >  1:1713025/1‑69 (MQ=255)

cACGGCGATAGCACCACAATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATgg                                                                   >  1:471535/1‑69 (MQ=255)

cACGGCGATAGCACCACAATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATgg                                                                   >  1:1425762/1‑69 (MQ=255)

         aGCACCACAATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCt                                                          >  1:2051733/1‑69 (MQ=255)

         aGCACCACAATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCt                                                          >  1:905975/1‑69 (MQ=255)

             ccacAATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACg                                                      <  1:232992/69‑1 (MQ=255)

              cacaATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGc                                                     <  1:2296277/69‑1 (MQ=255)

              cacaATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGc                                                     <  1:2857933/69‑1 (MQ=255)

              cacaATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGc                                                     <  1:1252453/69‑1 (MQ=255)

               acaATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCa                                                    >  1:1060936/1‑69 (MQ=255)

               acaATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCa                                                    >  1:35044/1‑69 (MQ=255)

               acaATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCa                                                    >  1:1867018/1‑69 (MQ=255)

               acaATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCa                                                    >  1:1011222/1‑69 (MQ=255)

                  aTACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGt                                                  >  1:1778498/1‑68 (MQ=255)

                  aTACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGt                                                  >  1:743705/1‑68 (MQ=255)

                     cAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTgaa                                               >  1:2115705/1‑66 (MQ=255)

                         gCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTaa                                          >  1:740331/1‑69 (MQ=255)

                               tGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACtttt                                     >  1:3360435/1‑68 (MQ=255)

                               tGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACtttt                                     >  1:3065785/1‑68 (MQ=255)

                                    gcagATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAgg                               >  1:131365/1‑69 (MQ=255)

                                    gcagATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAgg                               >  1:424273/1‑69 (MQ=255)

                                    gcagATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCT‑CTTACGCAGTGCGATTAACTTTTGGTAgg                               >  1:1296103/1‑68 (MQ=255)

                                    gcagATCCTGGTAATTGCCCCATGTCAGGATGGCTTACTGCTTACGCAGTGCGATTAACTTTTGGTAgg                               >  1:564875/1‑69 (MQ=255)

                                     cagATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTgg                                   <  1:2353486/64‑1 (MQ=255)

                                     cagATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTgg                                   <  1:2478085/64‑1 (MQ=255)

                                     cagATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTgg                                   <  1:986331/64‑1 (MQ=255)

                                     cagATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTgg                                   <  1:1615826/64‑1 (MQ=255)

                                     cagATCCTGGTAATTGCCCCATGTCAGGACGGCTTCCTGCTTACGCAGTGCGTTTAACTTTTgg                                   <  1:2948535/64‑1 (MQ=255)

                                          ccTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTaa                          >  1:1983799/1‑68 (MQ=255)

                                          ccTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTaa                          >  1:2653615/1‑68 (MQ=255)

                                           cTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTaaaa                        >  1:2868556/1‑69 (MQ=255)

                                                aaTTGCCCCATGTCAGGATGGCTTCCTGCTTACGc                                                     <  1:1978627/35‑1 (MQ=255)

                                                   cgCCCCATGTCAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACAGAgg                <  1:1580513/68‑1 (MQ=255)

                                                   cgCCCCATGTCAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACAGAgg                <  1:1825451/68‑1 (MQ=255)

                                                   cgCCCCATGTCAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACAGAgg                <  1:2540014/68‑1 (MQ=255)

                                                   cgCCCCATGTCAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACAGAgg                <  1:917058/68‑1 (MQ=255)

                                                   cgCCCCATGTCAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACAGAgg                <  1:2668238/68‑1 (MQ=255)

                                                   cgCCCCATGTCAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACAGAgg                <  1:1184488/68‑1 (MQ=255)

                                                   cgCCCCATGTCAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACAGAgg                <  1:901110/68‑1 (MQ=255)

                                                       ccATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAatc            <  1:426217/69‑1 (MQ=255)

                                                       ccATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAatc            <  1:1863581/69‑1 (MQ=255)

                                                       ccATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAatc            <  1:1229636/69‑1 (MQ=255)

                                                       ccATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAatc            <  1:87016/69‑1 (MQ=255)

                                                       ccATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAatc            <  1:2441048/69‑1 (MQ=255)

                                                       ccATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAatc            <  1:211636/69‑1 (MQ=255)

                                                            tCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAATCATCg        >  1:1194302/1‑68 (MQ=255)

                                                            tCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAATCATCg        >  1:2817619/1‑68 (MQ=255)

                                                            tCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAATCATCg        >  1:2813752/1‑68 (MQ=255)

                                                            tCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAATCATCg        >  1:54364/1‑68 (MQ=255)

                                                            tCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAATCATCg        >  1:3416036/1‑68 (MQ=255)

                                                            tCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAATCATCg        >  1:2000140/1‑68 (MQ=255)

                                                            tCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAATCATCg        >  1:1370549/1‑68 (MQ=255)

                                                            tCAGGATGGCTTCCTGCTTACGCAGTGCGACTAACTTTTGGTAGGTGTAAAACACCGAGGAATCATCg        >  1:3391686/1‑68 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGgt                              >  1:1146487/1‑45 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGACTCATCg        >  1:451272/1‑67 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGACTCATCg        >  1:1503914/1‑67 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGACTCATCg        >  1:1249579/1‑67 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGACTCATCg        >  1:683474/1‑67 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGACTCATCg        >  1:737279/1‑67 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGACTCATCg        >  1:3280289/1‑67 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGACTCATCg        >  1:1873509/1‑67 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGACTCATCg        >  1:195109/1‑67 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGACTCATCg        >  1:3055097/1‑67 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGACTCATCg        >  1:2668579/1‑67 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGACTCATCg        >  1:2636178/1‑67 (MQ=255)

                                                             cAGGACGGCTTCTTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGACTCATCg        >  1:2368626/1‑67 (MQ=255)

                                                                 aTGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAATCATCGGCCAgc  >  1:3296692/1‑69 (MQ=255)

CACGGCGATAGCACCACAATACAGGGCTGTTTGGCAGCAGATCCTGGTAATTGCCCCATGTCAGGATGGCTTCCTGCTTACGCAGTGCGATTAACTTTTGGTAGGTGTAAAACACCGAGGAATCATCGGCCAGC  >  minE/2904617‑2904750

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