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
A8 F50 I1 R1	163	55.0	1534755	98.6%	1513268	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,147,149	A→G	pseudogene (124/417 nt)	yghX ←	pseudogene, dienlactone hydrolase family

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,147,149	0	A	G	97.6%	122.5 / NA	41	pseudogene (124/417 nt)	yghX	pseudogene, dienlactone hydrolase family
Reads supporting (aligned to +/- strand): ref base A (0/0); major base G (18/22); minor base C (0/1); total (18/23)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGCCGCCTCGTAAGCAGGCCAGCCCTCGTTGATTCGGGTGTCCAGTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAATCATTCATCAGTTTGTTGGATCAACCTGCTGTT  >  NC_000913/3147005‑3147291

aCGCCGCCTCGTAAGCAGGCCAGCCCTCGTTGATTCGGGTGTCCAGTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGAc                                                                                                                                          >  2:134171/1‑151 (MQ=255)

             aGCAGGCCAGCCCTCGTTGATTCGGGTGTCCAGTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTc                                                                                                                             <  1:516391/151‑1 (MQ=255)

                aGGCCAGCCCTCGTTGATTCGGGTGTCCAGTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGa                                                                                                                           >  2:402170/1‑150 (MQ=255)

                  gCCAGCCCTCGTTGATTCGGGTGTCCAGTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATAc                                                                                                                        >  2:362985/1‑151 (MQ=255)

                           cGTTGATTCGGGTGTCCAGTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCg                                                                                                                 <  2:496987/149‑1 (MQ=255)

                           cGTTGATTCGGGTGTCCAGTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCg                                                                                                                 <  2:127487/149‑1 (MQ=255)

                           cGTTGATTCGGGTGTCCAGTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGcc                                                                                                               <  1:209876/151‑1 (MQ=255)

                                aTTCGGGTGTCCAGTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGc                                                                                                          >  2:492566/1‑151 (MQ=255)

                                          ccAGTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCg                                                                                                  <  2:198331/149‑1 (MQ=255)

                                          ccAGTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGt                                                                                                <  1:65636/151‑1 (MQ=255)

                                            aGTTCCGCGAAGTGGAGTAGTAAAGGCGCTACACTCTCCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCCCCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCTTCCGTTCCGCCCCCGCCATAGCAAAATCCGGTaa                                                                                              <  1:397332/151‑1 (MQ=255)

                                             gTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAAt                                                                                             >  2:402548/1‑151 (MQ=255)

                                              ttCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTCCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAAt                                                                                             <  1:525531/150‑1 (MQ=255)

                                                  gcgAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATAccc                                                                                         >  1:529366/1‑150 (MQ=255)

                                                  gcgAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATAccc                                                                                         >  2:450030/1‑150 (MQ=255)

                                                    gAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACt                                                                                      >  2:675380/1‑151 (MQ=255)

                                                              agtaAAGGCGCTTCAATCTCCGCCACATCGGCAGTGGGTCCCTCACGCCAATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTc                                                                             <  2:561358/150‑1 (MQ=255)

                                                                 aaaGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGCCCATAAAACGGCCCCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCt                                                                          <  2:308510/150‑1 (MQ=255)

                                                                 aaaGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCCCCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGt                                                                              <  1:163349/146‑1 (MQ=255)

                                                                         ttCAATCTTCGCCACAGCGGCGGTGGGTGCCTGACGACCATAAAACGGCCCCGCGCAGGCCATTTCCGGAGCCGCGACAGCCGCCGCGTTCGATCCGCCCCCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCgg                                                                     <  2:403836/147‑1 (MQ=255)

                                                                             aTCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGtt                                                             >  1:513690/1‑151 (MQ=255)

                                                                                ttCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGc                                                           >  1:436220/1‑150 (MQ=255)

                                                                                          cGGCAGTGGGTGCCTGACGACCATAAAACGGCCCCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCTTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCa                                                  <  2:128808/149‑1 (MQ=255)

                                                                                            gCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTg                                              >  2:749231/1‑151 (MQ=255)

                                                                                             cAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGc                                             >  1:658588/1‑151 (MQ=255)

                                                                                                   gTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCaaa                                       <  1:450051/151‑1 (MQ=255)

                                                                                                     gCCTGACGACCATAAAACGGCCCCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAAt                                                <  1:238089/140‑1 (MQ=255)

                                                                                                     gCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAAt                                                >  2:238080/1‑140 (MQ=255)

                                                                                                      ccTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGa                                     <  1:112261/150‑1 (MQ=255)

                                                                                                          acgacCAAAAAACGGCACCGCGCGGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATCCGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCaaa                                       <  2:607178/144‑1 (MQ=255)

                                                                                                            gacCATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAAtca                                <  1:113516/149‑1 (MQ=255)

                                                                                                             acCATAAAACGGCACCGCGCAGCCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAAtcatt                              <  1:622202/150‑1 (MQ=255)

                                                                                                               cATAAAACGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAAtcattcat                           >  1:134692/1‑151 (MQ=255)

                                                                                                                  aaaaCGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAATCATtcatc                          >  2:462175/1‑149 (MQ=255)

                                                                                                                   aaaCGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAATCATTCATCAGt                       <  2:484026/151‑1 (MQ=255)

                                                                                                                   aaaCGGCACCGCGCAGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAATCATTCATCAGt                       >  2:604239/1‑151 (MQ=255)

                                                                                                                           ccGCGCGGGCCAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAATCATTCATCAGTttgttg                 <  2:122479/149‑1 (MQ=255)

                                                                                                                             tcccgatctaGTCCCGGATGCGCGACAGCCGCCGCTTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAATCATTCATCAGTttgtt                  <  2:123531/137‑1 (MQ=255)

                                                                                                                                    ccAGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAATCATTCATCAGTTTGTTGGATCAACctgc      >  1:574946/1‑151 (MQ=255)

                                                                                                                                      aGTTCCGGATGCGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAATCATTCATCAGTttgtt                  >  1:123534/1‑137 (MQ=255)

                                                                                                                                          ccGGATGCGCGACAGCCGCCGCGTTCGATCCGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAATCATTCATCAGTTTGTTGGATCAACCTGCTGtt  <  1:402191/149‑1 (MQ=255)

ACGCCGCCTCGTAAGCAGGCCAGCCCTCGTTGATTCGGGTGTCCAGTTCCGCGAAGTGGAGTAGTAAAGGCGCTTCAATCTTCGCCACATCGGCAGTGGGTGCCTGACGACCATAAAACGGCACCGCGCAGGCCAGTTCCGGATACGCGACAGCCGCCGCGTTCGATACGCCACCGCCATAGCAAAATCCGGTAATACCCACTTTGCCTGTCGCTTGCGGATAGCGTTGCATAAACTCAATTGCGGCAAAGAAATCATTCATCAGTTTGTTGGATCAACCTGCTGTT  >  NC_000913/3147005‑3147291

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A