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	1,315,909	G→A	22.4%	L169L (CTG→CTA)	hisA →	N‑(5'‑phospho‑L‑ribosyl‑formimino)‑5‑amino‑1‑ (5'‑phosphoribosyl)‑4‑imidazolecarboxamide isomerase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,315,909	0	G	A	22.4%	96.6 / 19.2	71	L169L (CTG→CTA)	hisA	N‑(5'‑phospho‑L‑ribosyl‑formimino)‑5‑amino‑1‑ (5'‑phosphoribosyl)‑4‑imidazolecarboxamide isomerase
Reads supporting (aligned to +/- strand): ref base G (35/20); new base A (5/11); total (40/31)
Fisher's exact test for biased strand distribution p-value = 4.28e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.77e-01

GAGAACTCGGGCGTTTCACTGGAACAACTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTTATATGAAGAAGTGTG  >  minE/1315841‑1315974

gagaACTCGGGCGTTTCACTGGAACAACTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCtg                                                                   <  1:50379/69‑1 (MQ=255)

gagaACTCGGGCGTTTCACTGGAACAACTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCtg                                                                   <  1:501934/69‑1 (MQ=255)

gagaACTCGGGCGTTTCACTGGAACAACTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCtg                                                                   <  1:2296508/69‑1 (MQ=255)

gagaACTCGGGCGTTTCACTGGAACAACTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCtg                                                                   <  1:1352893/69‑1 (MQ=255)

gagaACTCGGGCGTTTCACTGGAACAACTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCtg                                                                   <  1:2695178/69‑1 (MQ=255)

                       acaacTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGAc                                              <  1:1464400/67‑1 (MQ=255)

                          acTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCTACGGCAc                                         >  1:308032/1‑69 (MQ=255)

                          acTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCa                                          >  1:1786724/1‑68 (MQ=255)

                          acTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCAc                                         >  1:1564436/1‑69 (MQ=255)

                          acTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCAc                                         >  1:1085108/1‑69 (MQ=255)

                          acTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCAc                                         >  1:575551/1‑69 (MQ=255)

                          acTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCAc                                         >  1:2378882/1‑69 (MQ=255)

                          acTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCAc                                         >  1:399113/1‑69 (MQ=255)

                          acTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCAc                                         >  1:360008/1‑69 (MQ=255)

                          acTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCAc                                         >  1:728662/1‑69 (MQ=255)

                          acTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCAc                                         >  1:1256995/1‑69 (MQ=255)

                          acTGGTGGAAACCTATATGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCAc                                         >  1:920225/1‑69 (MQ=255)

                                 gAACCCTATCTGCCCGTCGGCCTGAAACATGTACTGTGTACCGATATCTCGCGCGAc                                              >  1:2700697/1‑57 (MQ=255)

                                 gAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATAtctc                                                     >  1:2718577/1‑50 (MQ=255)

                                 gAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGc                                   >  1:3270529/1‑68 (MQ=255)

                                 gAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTATGTACCGATATCTCGCGCGCCGGCACGCTGGc                                   >  1:1788339/1‑68 (MQ=255)

                                 gAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGc                                   >  1:1018727/1‑68 (MQ=255)

                                 gAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGc                                   >  1:2547188/1‑68 (MQ=255)

                                 gAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGc                                   >  1:482039/1‑68 (MQ=255)

                                 gAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGc                                   >  1:701196/1‑68 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTgg                                    >  1:1529042/1‑62 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGc                               >  1:2166675/1‑67 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGc                               >  1:3262602/1‑67 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGc                               >  1:2898482/1‑67 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGc                               >  1:1192337/1‑67 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGc                               >  1:3414837/1‑67 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGc                               >  1:352050/1‑67 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGc                               >  1:1261887/1‑67 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGc                               >  1:1312801/1‑67 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGc                               >  1:2614664/1‑67 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGc                               >  1:404708/1‑67 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGc                               >  1:1637122/1‑67 (MQ=255)

                                      cTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACAGATAtct                                                      >  1:1549884/1‑44 (MQ=255)

                                       tATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGTCAGGctct                            <  1:2321769/69‑1 (MQ=255)

                                       tATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGctct                            <  1:1221250/69‑1 (MQ=255)

                                       tATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGctct                            <  1:530093/69‑1 (MQ=255)

                                       tATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGctct                            <  1:2806994/69‑1 (MQ=255)

                                       tATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGctct                            <  1:282054/69‑1 (MQ=255)

                                       tATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGctct                            <  1:2195704/69‑1 (MQ=255)

                                       tATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGctct                            <  1:786666/69‑1 (MQ=255)

                                        aTCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGctct                            <  1:556360/68‑1 (MQ=255)

                                        aTCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGctct                            <  1:2091877/68‑1 (MQ=255)

                                           tGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACg                        >  1:500571/1‑69 (MQ=255)

                                           tGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACg                        >  1:94194/1‑69 (MQ=255)

                                           tGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACg                        >  1:1905805/1‑69 (MQ=255)

                                           tGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACg                        >  1:2056397/1‑69 (MQ=255)

                                              ccGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAg                                 >  1:2664713/1‑57 (MQ=255)

                                                   ggCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTta                <  1:3291083/69‑1 (MQ=255)

                                                    gCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGCggg                                <  1:2282687/52‑1 (MQ=255)

                                                    gCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGCggg                                <  1:1077941/52‑1 (MQ=255)

                                                    gCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGCggg                                <  1:927434/52‑1 (MQ=255)

                                                    gCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGCggg                                <  1:1081333/52‑1 (MQ=255)

                                                    gCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGCggg                                <  1:1118527/52‑1 (MQ=255)

                                                    gCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGCggg                                <  1:67825/52‑1 (MQ=255)

                                                    gCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGCggg                                <  1:3111488/52‑1 (MQ=255)

                                                    gCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGCggg                                <  1:2300848/52‑1 (MQ=255)

                                                    gCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGCggg                                <  1:3427236/52‑1 (MQ=255)

                                                    gCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGCACGCTGGCggg                                <  1:2710114/52‑1 (MQ=255)

                                                    gCCTGAAACATGTGCTATGTACCGATATCTCGCGCGACGGAACGCTGGCggg                                <  1:2695868/52‑1 (MQ=255)

                                                      cTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTta                >  1:2500532/1‑66 (MQ=255)

                                                      cTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTta                >  1:660868/1‑66 (MQ=255)

                                                      cTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTta                >  1:3016829/1‑66 (MQ=255)

                                                       tGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTTATATg            <  1:487903/69‑1 (MQ=255)

                                                       tGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTTATATg            <  1:2524973/69‑1 (MQ=255)

                                                       tGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTTATATg            <  1:2029192/69‑1 (MQ=255)

                                                       tGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTTATATg            <  1:2599764/69‑1 (MQ=255)

                                                       tGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTTATATg            <  1:616246/69‑1 (MQ=255)

                                                       tGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTTATATg            <  1:126681/69‑1 (MQ=255)

                                                       tGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTTATATg            <  1:3001525/69‑1 (MQ=255)

                                                              tgtgCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTTATATgaa          <  1:1612463/64‑1 (MQ=255)

                                                                  cTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTTATATGAAGAAGtgtg  <  1:1866283/68‑1 (MQ=255)

GAGAACTCGGGCGTTTCACTGGAACAACTGGTGGAAACCTATCTGCCCGTCGGCCTGAAACATGTGCTGTGTACCGATATCTCGCGCGACGGCACGCTGGCAGGCTCTAACGTCTCTTTATATGAAGAAGTGTG  >  minE/1315841‑1315974

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A