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 F28 I1 R1	162	93.0	3098984	99.0%	3067994	139.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,604,295	T→C	G83G (GGT→GGC)	lsrD →	Autoinducer‑2 ABC transporter membrane subunit LsrD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,604,295	0	T	C	97.9%	162.5 / ‑4.5	47	G83G (GGT→GGC)	lsrD	Autoinducer‑2 ABC transporter membrane subunit LsrD
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (11/35); total (11/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01

CAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTG  >  NC_000913/1604163‑1604425

cAGTGACTTTGTCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGa                                                                                                                             <  2:671594/140‑1 (MQ=255)

  gTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTTTTTTGGTTCGACCATCGGCCTCTGCGCCCTTGCATTGGGGGGACTGTTTTTAAATGGGGGGCCgccg                                                                                                                           >  2:171512/1‑137 (MQ=255)

    gACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGcc                                                                                                                         <  1:1040849/140‑1 (MQ=255)

           ccTGCATTGGCATTGTCGCCCTGCCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCg                                                                                                                  <  1:1052427/139‑1 (MQ=255)

            cTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGa                                                                                                                 <  1:395810/140‑1 (MQ=255)

            cTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGa                                                                                                                 <  2:1094651/140‑1 (MQ=255)

            cTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGa                                                                                                                 <  2:19825/140‑1 (MQ=255)

            cTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGa                                                                                                                 <  2:728531/140‑1 (MQ=255)

                          tCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTa                                                                                                   <  1:250836/140‑1 (MQ=255)

                            gCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACt                                                                                                 <  2:543796/140‑1 (MQ=255)

                              ccTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGc                                                                                               <  1:30565/140‑1 (MQ=255)

                               cTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCt                                                                                              <  1:913382/140‑1 (MQ=255)

                                     cTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGgcgc                                                                                        <  1:171512/140‑1 (MQ=255)

                                     cTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGgcgc                                                                                        <  2:258696/140‑1 (MQ=255)

                                      tAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCa                                                                                       <  1:311791/140‑1 (MQ=255)

                                      tAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCa                                                                                       <  1:606255/140‑1 (MQ=255)

                                      tAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCa                                                                                       <  1:551848/140‑1 (MQ=255)

                                        aCGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCAtt                                                                                     <  1:551100/140‑1 (MQ=255)

                                           aTGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATtgtg                                                                                  <  2:1131570/140‑1 (MQ=255)

                                            tGGTGATTGTCAGTGGCGGGGTCGATATTTTGTTTGGTTCGCCCATCGGCCCCTGCGCCATTGCATTGGGGGGTCTGTTTCAAAGTGGCGGGCCCCTGCCGCCGGGGGTAGCCCCGACCCTACTCCTCGGCGCAAtgggg                                                                                 >  2:1209144/1‑137 (MQ=255)

                                             ggTGATTGTCAGTGGCGGGGTCGATATTTTGTTTTGTTCGACCATCGGCCCCTGCGCCATTGCATTGGGCGTACTGTTTTTAAAAGGCGGGCCGATGCCGCCTGCGGTAATCCCGACCCTACTTCTCGGGGCATtttggg                                                                                >  2:797376/1‑138 (MQ=255)

                                               tGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCggg                                                                              <  1:364567/140‑1 (MQ=255)

                                                          ggCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGc                                                                   <  1:377829/140‑1 (MQ=255)

                                                              ggATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGa                                                               <  2:1303023/140‑1 (MQ=255)

                                                                      atTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTTCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTAt                                                       <  1:1075640/140‑1 (MQ=255)

                                                                      atTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTAt                                                       <  2:541824/140‑1 (MQ=255)

                                                                      atTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTAt                                                       <  1:1420429/140‑1 (MQ=255)

                                                                          cGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCtat                                                   >  1:1011785/1‑140 (MQ=255)

                                                                          cGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCtat                                                   >  1:194865/1‑140 (MQ=255)

                                                                            tttGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATAc                                                 <  1:990976/140‑1 (MQ=255)

                                                                                      ccATCGGCCTCTGTGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATCCTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAAc                                       <  1:808846/140‑1 (MQ=255)

                                                                                         tCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCg                                    >  1:600602/1‑140 (MQ=255)

                                                                                          cGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGc                                   >  2:859640/1‑140 (MQ=255)

                                                                                          cGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGc                                   <  1:423417/140‑1 (MQ=255)

                                                                                           ggCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCt                                  <  1:490130/140‑1 (MQ=255)

                                                                                           ggCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCt                                  <  2:194865/140‑1 (MQ=255)

                                                                                                 tGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGAt                            >  2:136098/1‑140 (MQ=255)

                                                                                                 tGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGAt                            >  2:213540/1‑140 (MQ=255)

                                                                                                           cattgGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGc                  <  1:1209144/140‑1 (MQ=255)

                                                                                                            attgGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCa                 <  1:396357/140‑1 (MQ=255)

                                                                                                            attgGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCa                 <  1:55399/140‑1 (MQ=255)

                                                                                                            attgGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCa                 <  1:797376/140‑1 (MQ=255)

                                                                                                            attgGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCa                 <  2:760575/140‑1 (MQ=255)

                                                                                                             ttgGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCAc                <  1:367414/140‑1 (MQ=255)

                                                                                                              tgGGCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATTCCAAAGTTAACCCGCTGGTGATTACGCTTGACACg               <  1:163485/140‑1 (MQ=255)

                                                                                                                ggCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCt             >  1:757906/1‑140 (MQ=255)

                                                                                                                ggCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCt             >  2:766178/1‑140 (MQ=255)

                                                                                                                ggCGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCt             >  1:147261/1‑140 (MQ=255)

                                                                                                                  cGTACTGTTTCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGt           >  2:247093/1‑140 (MQ=255)

                                                                                                                           tCAAAGTGGCGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACACTTGGCACGCTGTATCTGTTTg  >  1:955200/1‑140 (MQ=255)

CAGTGACTTTATCTGCATTGGCATTGTCGCCCTACCGCTAACGATGGTGATTGTCAGTGGCGGGATCGATATTTCGTTTGGTTCGACCATCGGCCTCTGCGCCATTGCATTGGGCGTACTGTTTCAAAGTGGTGTGCCGATGCCGCTGGCGATACTCCTGACCTTACTGCTCGGCGCATTGTGCGGGCTGATCAACGCCGGATTAATTATCTATACCAAAGTTAACCCGCTGGTGATTACGCTTGGCACGCTGTATCTGTTTG  >  NC_000913/1604163‑1604425

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 33 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A