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	2,254,185	T→C	29.3%	Q951Q (CAA→CAG)	rpoC ←	RNA polymerase, beta prime subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,254,185	0	T	C	29.3%	88.6 / 41.7	92	Q951Q (CAA→CAG)	rpoC	RNA polymerase, beta prime subunit
Reads supporting (aligned to +/- strand): ref base T (52/13); new base C (14/13); total (66/26)
Fisher's exact test for biased strand distribution p-value = 1.04e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

AGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGATGTGGAACGTACGCAT  >  minE/2254120‑2254244

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:971579/1‑69 (MQ=255)

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:2232076/1‑69 (MQ=255)

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:2575927/1‑69 (MQ=255)

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:2691212/1‑69 (MQ=255)

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:2709607/1‑69 (MQ=255)

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:206788/1‑69 (MQ=255)

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:178464/1‑69 (MQ=255)

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:333695/1‑69 (MQ=255)

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:342454/1‑69 (MQ=255)

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:3429274/1‑69 (MQ=255)

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:925812/1‑69 (MQ=255)

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:1433864/1‑69 (MQ=255)

aGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACCTgg                                                          >  1:629708/1‑69 (MQ=255)

aGTTTACAGCTGGAGTTCACAACCGACTTCACCTAGCTGAGCTTGATGCTACCTTTGTATATCACCTg                                                           >  1:2537169/1‑68 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTcagcag                                          >  1:774742/1‑68 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCagcagc                                         >  1:190799/1‑69 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCagcagc                                         >  1:2823099/1‑69 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCagcagc                                         >  1:762775/1‑69 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCagcagc                                         >  1:3167225/1‑69 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCagcagc                                         >  1:201510/1‑69 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCagcagc                                         >  1:2550378/1‑69 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCagcagc                                         >  1:1967845/1‑69 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCagcagc                                         >  1:1823926/1‑69 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCagcagc                                         >  1:34094/1‑69 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCagcagc                                         >  1:1458953/1‑69 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCagcagc                                         >  1:604308/1‑69 (MQ=255)

                 cacaACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCagcagc                                         >  1:1547111/1‑69 (MQ=255)

                    aaCCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGc                                      >  1:1947338/1‑69 (MQ=255)

                    aaCCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGc                                      >  1:3077649/1‑69 (MQ=255)

                    aaCCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGc                                      >  1:358619/1‑69 (MQ=255)

                    aaCCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGc                                      >  1:885995/1‑69 (MQ=255)

                      ccGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCAc                                    <  1:57461/69‑1 (MQ=255)

                      ccGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCAc                                    <  1:2483312/69‑1 (MQ=255)

                        gACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACga                                  <  1:1028858/69‑1 (MQ=255)

                        gACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACga                                  <  1:328124/69‑1 (MQ=255)

                        gACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACga                                  <  1:3368703/69‑1 (MQ=255)

                        gACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACga                                  <  1:2499658/69‑1 (MQ=255)

                        gACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACga                                  <  1:580841/69‑1 (MQ=255)

                        gACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACga                                  <  1:214431/69‑1 (MQ=255)

                        gACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACga                                  <  1:2335805/69‑1 (MQ=255)

                        gACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACga                                  <  1:1539601/69‑1 (MQ=255)

                        gACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACga                                  <  1:2253882/69‑1 (MQ=255)

                        gACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACga                                  <  1:1097149/69‑1 (MQ=255)

                           ttCACGTTGCTGAGCTTGATTCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGAt                               >  1:2171059/1‑69 (MQ=255)

                           ttCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGGAGCCGCACGAGAt                               >  1:3041654/1‑69 (MQ=255)

                           ttCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGAt                               >  1:414739/1‑69 (MQ=255)

                           ttCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGAt                               >  1:79057/1‑69 (MQ=255)

                           ttCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGAt                               >  1:1547457/1‑69 (MQ=255)

                           ttCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGAt                               >  1:2485941/1‑69 (MQ=255)

                           ttCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGAt                               >  1:2762094/1‑69 (MQ=255)

                             cACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGc                             >  1:1978377/1‑69 (MQ=255)

                             cACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGc                             >  1:32346/1‑69 (MQ=255)

                             cACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGc                             >  1:1427772/1‑69 (MQ=255)

                             cACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGc                             >  1:726478/1‑69 (MQ=255)

                                         ctagATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:1465135/4‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGa                  >  1:3115080/1‑68 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGa                  >  1:2139029/1‑68 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGa                  <  1:613335/68‑1 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:3082771/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:3377442/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:1617432/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:1695601/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:683293/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:2979767/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:1332149/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:2638396/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:2571205/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:2529078/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:2510151/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:2307570/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:1029217/1‑69 (MQ=255)

                                         cTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGAt                 >  1:234407/1‑69 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTcagc                                            <  1:1307534/39‑1 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTcagc                                            <  1:1010905/39‑1 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTcagc                                            <  1:2738607/39‑1 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTcagc                                            <  1:2412799/39‑1 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTcagc                                            <  1:251186/39‑1 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTcagc                                            <  1:2288429/39‑1 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTcagc                                            <  1:2205388/39‑1 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTcagc                                            <  1:2188345/39‑1 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTcagc                                            <  1:2989865/39‑1 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTcagc                                            <  1:3034452/39‑1 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTcagc                                            <  1:3238723/39‑1 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTcagc                                            <  1:3260915/39‑1 (MQ=255)

                                            gATGCTACCTTTGTTTTTCACCTGGATGCTGGATTaagc                                            <  1:2454275/39‑1 (MQ=37)

                                                cTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGATGTGGaa           >  1:1751831/1‑68 (MQ=255)

                                                     tttGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCg                           >  1:2033874/1‑47 (MQ=255)

                                                     tttGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGa                  >  1:963102/1‑56 (MQ=255)

                                                     tttGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGATGTGGAACGTACg     >  1:1518675/1‑69 (MQ=255)

                                                     tttGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACAGATGTGGAACGTACg     >  1:1739778/1‑69 (MQ=255)

                                                        gTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGATGTGGAACGTACGCAt  >  1:1775941/1‑69 (MQ=255)

                                                        gTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACAGATGTGGAACGTACGCa   >  1:815741/1‑68 (MQ=255)

AGTTTACCGCTGGAGTTCACAACCGACTTCACGTTGCTGAGCTTGATGCTACCTTTGTTTTTCACTTGGATGCTGGATTCAGCAGCCGCACGAGATGCCGCACCACCGATGTGGAACGTACGCAT  >  minE/2254120‑2254244

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