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
A4 F21 I0 R1	1009	73.8	4146436	87.4%	3623985	60.3

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	2,040,951	T→A	20.4%	*120K (TAA→AAA)	yqiH →	predicted periplasmic pilin chaperone

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	2,040,951	0	T	A	20.4%	174.5 / 38.6	78	*120K (TAA→AAA)	yqiH	predicted periplasmic pilin chaperone
Reads supporting (aligned to +/- strand): ref base T (26/36); new base A (11/5); total (37/41)
Fisher's exact test for biased strand distribution p-value = 9.05e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAAAAAATTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTGGCGGCC  >  minE/2040882‑2041015

gAAAAAATTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTa                                                                 <  1:3324071/71‑1 (MQ=255)

  aaaaaTTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCaaaa                                                               >  1:1388890/1‑71 (MQ=255)

  aaaaaTTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTaaa                                                               <  1:54073/71‑1 (MQ=255)

  aaaaaTTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTa                                                                 <  1:3269558/69‑1 (MQ=255)

  aaaaaTTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGACCTa                                                                 <  1:3406544/69‑1 (MQ=255)

         gCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATa                                                         <  1:912643/70‑1 (MQ=255)

             aaCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATaaaaaa                                                    <  1:2115380/71‑1 (MQ=255)

             aaCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaa                                                     >  1:1579638/1‑70 (MQ=255)

              aCTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATaaaaaaa                                                   <  1:3394528/71‑1 (MQ=255)

                 tCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTaaa                                                               >  1:1244895/1‑56 (MQ=255)

                   cTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAAtgt                                               <  1:2319009/70‑1 (MQ=255)

                    tAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGa                                             >  1:1339877/1‑71 (MQ=255)

                      aaGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCaaaa                                                               >  1:3415474/1‑51 (MQ=255)

                      aaGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATaa                                                        >  1:3853842/1‑58 (MQ=255)

                      aaGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATg                                           <  1:2018164/71‑1 (MQ=255)

                      aaGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGAt                                            <  1:61387/70‑1 (MQ=255)

                       aGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGc                                          <  1:1254894/71‑1 (MQ=255)

                       aGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGc                                          <  1:2337742/71‑1 (MQ=255)

                       aGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGc                                          <  1:2264877/71‑1 (MQ=255)

                            gagaAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTc                                     <  1:2465925/71‑1 (MQ=255)

                             agaAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCa                                    >  1:3544347/1‑71 (MQ=255)

                              gaAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGa                                             >  1:217341/1‑61 (MQ=255)

                              gaAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCAc                                   <  1:1352312/71‑1 (MQ=255)

                              gaAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCAc                                   <  1:119157/71‑1 (MQ=255)

                              gaAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCAc                                   <  1:2612630/71‑1 (MQ=255)

                               aaaCGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAAt                                                 <  1:4126295/56‑1 (MQ=255)

                               aaaCGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCAc                                   <  1:3028560/70‑1 (MQ=255)

                               aaaCGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACt                                  <  1:2688349/71‑1 (MQ=255)

                                 aCGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATaaaaaaaa                                                  <  1:3161841/53‑1 (MQ=255)

                                 aCGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTAt                                <  1:359158/71‑1 (MQ=255)

                                  cGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATg                               >  1:579041/1‑71 (MQ=255)

                                   gCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATg                               >  1:3935384/1‑70 (MQ=255)

                                    ctctTCTATTTTAGCGTGCGAGAAATACCGCCCaaaa                                                               >  1:4037320/1‑37 (MQ=38)

                                    ctctTCTATTTTAACGTGCGAGAAATACCGCCCaaaa                                                               >  1:3047072/1‑37 (MQ=255)

                                    ctctTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATg                               >  1:1604086/1‑69 (MQ=255)

                                     tcttctATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCAc                                   <  1:3279383/64‑1 (MQ=255)

                                     tcttctATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCAc                                   <  1:3418878/64‑1 (MQ=255)

                                      cttctATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcag                            >  1:3921852/1‑70 (MQ=255)

                                       ttctATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcagca                          >  1:3596085/1‑71 (MQ=255)

                                       ttctATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcag                            <  1:1856895/69‑1 (MQ=255)

                                        tctATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAAtgt                                               <  1:2784611/49‑1 (MQ=255)

                                        tctATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCAc                         >  1:3990970/1‑71 (MQ=255)

                                         ctATTTTAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACg                        >  1:2360734/1‑71 (MQ=255)

                                          tATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCaa                                        >  1:2116121/1‑54 (MQ=255)

                                          tATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCaa                                        >  1:3847676/1‑54 (MQ=255)

                                           aTTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCa                      >  1:2823219/1‑71 (MQ=255)

                                           aTTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCa                      >  1:2704196/1‑71 (MQ=255)

                                           aTTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCa                      >  1:870075/1‑71 (MQ=255)

                                            ttttAACGTTCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATgc                              >  1:674423/1‑62 (MQ=255)

                                            ttttAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATgc                              >  1:883164/1‑62 (MQ=255)

                                             tttAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAAtgtg                                              <  1:594026/45‑1 (MQ=255)

                                             tttAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCAc                                   <  1:4072556/56‑1 (MQ=255)

                                             tttAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCAtt                    >  1:3260698/1‑71 (MQ=255)

                                              ttAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgc                              >  1:2074562/1‑60 (MQ=255)

                                              ttAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgc                              >  1:1799941/1‑60 (MQ=255)

                                              ttAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCa                      >  1:2138253/1‑68 (MQ=255)

                                               tAACGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGa                                             >  1:1037193/1‑44 (MQ=255)

                                                aaCGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcagca                          >  1:3122233/1‑62 (MQ=255)

                                                aaCGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcagca                          >  1:2014071/1‑62 (MQ=255)

                                                aaCGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGa                  <  1:1699539/70‑1 (MQ=255)

                                                  cGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAAc               <  1:1370413/71‑1 (MQ=255)

                                                  cGTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAAc               <  1:3700927/71‑1 (MQ=255)

                                                   gTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATg                               >  1:3877449/1‑54 (MQ=255)

                                                   gTGCGAGAAATACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAAc               >  1:2897705/1‑70 (MQ=255)

                                                    tGCGAGAAATACCGCCCTAAACAGATAAAAAAAAtgt                                               <  1:3243809/37‑1 (MQ=255)

                                                    tGCGAGAAATACCGCCCTAAACAGATAAAAAAAAtgt                                               <  1:2021430/37‑1 (MQ=255)

                                                    tGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTc                                     <  1:1060634/47‑1 (MQ=255)

                                                    tGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTAt                                <  1:3378644/52‑1 (MQ=255)

                                                         gaAATACCGCCCTAAACAGATAAAAAAAATGTGATg                                           >  1:3746403/1‑36 (MQ=255)

                                                         gaAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAg                                       >  1:3979035/1‑40 (MQ=255)

                                                         gaAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACg                        <  1:3966684/55‑1 (MQ=255)

                                                          aaaTACCGCCCAAAACAGATAAAAAAAATGTGATGCAAg                                       <  1:2096549/39‑1 (MQ=255)

                                                          aaaTACCGCCCAAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTgg       >  1:2757123/1‑71 (MQ=255)

                                                           aaTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTAt            <  1:1769995/65‑1 (MQ=255)

                                                           aaTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTggc      <  1:2739663/71‑1 (MQ=255)

                                                           aaTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTggc      <  1:3578868/71‑1 (MQ=255)

                                                            aTACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTggcg     >  1:801072/1‑71 (MQ=255)

                                                               ccGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgca                             >  1:1141601/1‑44 (MQ=255)

                                                                cGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTGGCGGcc  >  1:929403/1‑70 (MQ=255)

                                                                   ccTAAACAGATAAAAAAAATGTGATGCAAGTCACTa                                 >  1:3276224/1‑36 (MQ=255)

                                                                   ccTAAACAGATAAAAAAAATGTGATGCAAGTCACTATgcagca                          >  1:3074210/1‑43 (MQ=255)

                                                                    cTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTggcg     <  1:3143623/63‑1 (MQ=255)

                                                                     tAAACAGATAAAAAAAATGTGATGCAAGTCACTATg                               <  1:3743373/36‑1 (MQ=255)

                                                                     tAAACAGATAAAAAAAATGTGATGCAAGTCACTATg                               <  1:3151670/36‑1 (MQ=255)

GAAAAAATTGCTCAACTTCCTAAAGACAGAGAAACGCTCTTCTATTTTAACGTGCGAGAAATACCGCCCTAAACAGATAAAAAAAATGTGATGCAAGTCACTATGCAGCACGCATTGAAACTATTCTGGCGGCC  >  minE/2040882‑2041015

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