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	1,337,550	C→T	65.1%	R236H (CGT→CAT)	wcaE ←	predicted glycosyl transferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,337,550	0	C	T	65.1%	37.6 / 33.5	60	R236H (CGT→CAT)	wcaE	predicted glycosyl transferase
Reads supporting (aligned to +/- strand): ref base C (8/13); new base T (23/16); total (31/29)
Fisher's exact test for biased strand distribution p-value = 1.76e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01

ATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACTTTT  >  minE/1337493‑1337618

aTTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTa                                                             <  1:2206183/67‑1 (MQ=255)

aTTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTa                                                             <  1:301901/67‑1 (MQ=255)

aTTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTa                                                             <  1:2270075/67‑1 (MQ=255)

aTTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTa                                                             <  1:1317102/67‑1 (MQ=255)

   ggTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTAAAt                                                          >  1:715351/1‑67 (MQ=255)

      tttCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTAAATGCCAg                                                     <  1:636257/69‑1 (MQ=255)

      tttCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTAAATGCCAg                                                     >  1:1809435/1‑69 (MQ=255)

           ttATATTCAGACTTTGTTATCTAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTa                                                             <  1:1873849/56‑1 (MQ=255)

           ttATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTa                                                             <  1:2079538/56‑1 (MQ=255)

           ttATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTa                                                             <  1:1187356/56‑1 (MQ=255)

           ttATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTa                                                             <  1:373760/56‑1 (MQ=255)

           ttATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTa                                                             <  1:2623018/56‑1 (MQ=255)

           ttATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTa                                                             <  1:2985403/56‑1 (MQ=255)

                ttCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCg                                                               >  1:1216276/1‑49 (MQ=255)

                ttCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGt                                                              >  1:553383/1‑50 (MQ=255)

                ttCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGt                                                              >  1:1479999/1‑50 (MQ=255)

                ttCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGt                                                              >  1:1722399/1‑50 (MQ=255)

                ttCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGt                                                              >  1:1757541/1‑50 (MQ=255)

                ttCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGt                                                              >  1:1802206/1‑50 (MQ=255)

                                 aaGGCTTTCGTGTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:1141473/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCGAAAAGcc                                 >  1:2147969/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:3091607/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:2996410/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:3130657/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:2802098/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:2798806/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:2646398/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:336036/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:2302362/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:513585/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:600413/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:950569/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:2152023/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:2106011/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:172073/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:1776744/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:188069/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:1236198/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:167506/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:2021273/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 >  1:2093553/1‑62 (MQ=255)

                                 aaGGCTTTCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGc                                  >  1:1912304/1‑61 (MQ=255)

                                    gCTTTCGTCTTTGAGGTAGTACGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 <  1:774992/59‑1 (MQ=255)

                                    gCTTTCGTCTTTGAGGTAGTACGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGcc                                 <  1:590107/59‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:366441/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:3367583/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:1295788/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:511066/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:152936/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:3105417/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:1335603/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:1890696/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:1935311/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:2787900/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:2025393/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:755960/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:2356609/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:2320661/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:2036689/45‑1 (MQ=255)

                                       ttCGTCTTTGAGGTCGTATGTTGGCGTAAATGCCAGGATAATTCa                                            <  1:922864/45‑1 (MQ=255)

                                                         cGTTGGCGTAAATGCGAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACtttt  >  1:1339543/1‑69 (MQ=255)

                                                         cGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACtttt  >  1:1107000/1‑69 (MQ=255)

                                                         cGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACtttt  >  1:1619527/1‑69 (MQ=255)

                                                         cGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACtttt  >  1:16994/1‑69 (MQ=255)

                                                         cGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACtttt  >  1:2399955/1‑69 (MQ=255)

                                                         cGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACtttt  >  1:2194649/1‑69 (MQ=255)

                                                         cGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACttt   >  1:25493/1‑68 (MQ=255)

                                                         cGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACttt   >  1:2064853/1‑68 (MQ=255)

ATTGGTTTTCCTTATATTCAGACTTTGTTATATAAGGCTTTCGTCTTTGAGGTAGTACGTTGGCGTAAATGCCAGGATAATTCAGCCCAAAAGCCAGGCACATGTAATATTTGTCGTTGGACTTTT  >  minE/1337493‑1337618

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