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	1,322,814	A→G	39.4%	I40I (ATT→ATC)	galF ←	predicted subunit with GalU

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,322,814	0	A	G	39.4%	52.4 / 79.5	114	I40I (ATT→ATC)	galF	predicted subunit with GalU
Reads supporting (aligned to +/- strand): ref base A (17/52); new base G (31/14); total (48/66)
Fisher's exact test for biased strand distribution p-value = 5.35e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.78e-01

Only 100 of 114 total aligned reads displayed.

GCGTTCTTGGACGCGTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCTTAGT  >  minE/1322749‑1322873

gcgTTCTTGGACGCGTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATg                                                          <  1:3266192/69‑1 (MQ=255)

gcgTTCTTGGACGCGTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATg                                                          <  1:896299/69‑1 (MQ=255)

gcgTTCTTGGACGCGTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATg                                                          <  1:332532/69‑1 (MQ=255)

gcgTTCTTGGACGCGTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATg                                                          <  1:1354303/69‑1 (MQ=255)

gcgTTCTTGGACGCGTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATg                                                          <  1:432248/69‑1 (MQ=255)

gcgTTCTTGGACGCGTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATg                                                          <  1:369281/69‑1 (MQ=255)

gcgTTCTTGGACGCGTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTAGTCAAC‑AATg                                                          <  1:1093737/69‑1 (MQ=255)

         gaagcgTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑GATGTACTGAATc                                                 >  1:586643/4‑69 (MQ=255)

         gaagcgTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑GATGTACTGAATc                                                 >  1:1505847/4‑69 (MQ=255)

         gaagcgTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑GATGTACTGAATc                                                 >  1:1811701/4‑69 (MQ=255)

         gaagcgTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑GATGTACTGAATc                                                 >  1:1829900/4‑69 (MQ=255)

         gaagcgTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑GATGTACTGAATc                                                 >  1:1835454/4‑69 (MQ=255)

         gaagcgTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑GATGTACTGAATc                                                 >  1:769044/4‑69 (MQ=255)

         gaagcgTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑GATGTACTGAATc                                                 >  1:1957152/4‑69 (MQ=255)

         gaagcgTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑GATGTACTGAATc                                                 >  1:2132600/4‑69 (MQ=255)

         gaagcgTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑GATGTACTGAATc                                                 >  1:886721/4‑69 (MQ=255)

         gaagcgTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑GATGTACTGAATc                                                 >  1:2470214/4‑69 (MQ=255)

         gaagcgTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑GATGTACTGAATc                                                 >  1:2830712/4‑69 (MQ=255)

         gaagcgAGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑GATGTACTGAATc                                                 >  1:435584/4‑69 (MQ=255)

          aCGCGTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAAt                                                  <  1:3335036/67‑1 (MQ=255)

          aCGCGTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAAt                                                  <  1:145675/67‑1 (MQ=255)

                          gaggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAACAAATGTACTGAATc                                                 >  1:3001551/1‑53 (MQ=255)

                          gaggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATc                                                 >  1:600160/1‑52 (MQ=255)

                          gaggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATc                                                 <  1:53094/52‑1 (MQ=255)

                          gaggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATc                                                 >  1:3051187/1‑52 (MQ=255)

                          gaggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATc                                                 >  1:1505599/1‑52 (MQ=255)

                          gaggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATc                                                 >  1:2512067/1‑52 (MQ=255)

                          gaggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATc                                                 >  1:2299732/1‑52 (MQ=255)

                          gaggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATc                                                 <  1:2259220/52‑1 (MQ=255)

                          gaggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATc                                                 >  1:1217571/1‑52 (MQ=255)

                          gaggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATc                                                 >  1:1235418/1‑52 (MQ=255)

                          gaggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATc                                                 >  1:1925587/1‑52 (MQ=255)

                          gaggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTCAATc                                                 >  1:2822262/1‑52 (MQ=255)

                          gaggaTTTCTTTGATCCCTGAAGCCACAATCTCGTCAAC‑AATGTACTGatt                                                  >  1:11382/1‑49 (MQ=255)

                           aggaTTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATc                                                 <  1:1506860/51‑1 (MQ=255)

                               tttCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGt                            >  1:3018617/1‑68 (MQ=255)

                               tttCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGt                            >  1:3151088/1‑68 (MQ=255)

                                ttCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATg                                                          >  1:659967/1‑37 (MQ=255)

                                 tCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGc                         <  1:281044/69‑1 (MQ=255)

                                 tCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGc                         <  1:2717993/69‑1 (MQ=255)

                                 tCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGc                         <  1:1369868/69‑1 (MQ=255)

                                 tCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGc                         <  1:2357085/69‑1 (MQ=255)

                                 tCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCCACGATTGGTAGc                         <  1:500841/69‑1 (MQ=255)

                                 tCTTTGATCCCTGCAGCCACAATCTCATCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGc                         <  1:955442/69‑1 (MQ=255)

                                       aTCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCAtct                     <  1:932872/67‑1 (MQ=255)

                                       aTCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCAtct                     <  1:1043551/67‑1 (MQ=255)

                                       aTCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCAtct                     <  1:1906946/67‑1 (MQ=255)

                                       aTCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATCGGCTTGTCGACGATTGGTAGCAtct                     <  1:334774/67‑1 (MQ=255)

                                       aTCCCTGCAGCCACAATCTCATCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCAtct                     <  1:128591/67‑1 (MQ=255)

                                                  cacaATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGc        <  1:3142137/69‑1 (MQ=255)

                                                  cacaATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGc        <  1:1522053/69‑1 (MQ=255)

                                                  cacaATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGc        <  1:623961/69‑1 (MQ=255)

                                                  cacaATCTCGTCAAC‑AATGTACTGAATCATTGGATTGTCGACGATTGGTAGCATCTCTTTGGGTATCGc        <  1:8075/69‑1 (MQ=255)

                                                     aaTCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCtt     <  1:3048215/69‑1 (MQ=255)

                                                     aaTCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCtt     <  1:3052536/69‑1 (MQ=255)

                                                     aaTCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCtt     <  1:855889/69‑1 (MQ=255)

                                                     aaTCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCtt     <  1:417349/69‑1 (MQ=255)

                                                     aaTCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCtt     <  1:2637155/69‑1 (MQ=255)

                                                     aaTCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCtt     <  1:2858214/69‑1 (MQ=255)

                                                     aaTCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCtt     <  1:1268559/69‑1 (MQ=255)

                                                     aaTCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCtt     <  1:162715/69‑1 (MQ=255)

                                                     aaTCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCtt     <  1:181540/69‑1 (MQ=255)

                                                     aaTCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCtt     <  1:1234184/69‑1 (MQ=255)

                                                     aaTCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCtt     <  1:118408/69‑1 (MQ=255)

                                                     aaTCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCtt     <  1:2132728/69‑1 (MQ=255)

                                                      aTCTCGTCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCGGTAGCATCTCTTTGGGAATCGCCTTa    <  1:796206/69‑1 (MQ=255)

                                                      aTCTCGTCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCGGTAGCATCTCTTTGGGAATCGCCTTa    <  1:1265464/69‑1 (MQ=255)

                                                      aTCTCGTCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCGGTAGCATCTCTTTGGGAATCGCCTTa    <  1:38032/69‑1 (MQ=255)

                                                      aTCTCGTCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCGGTAGCATCTCTTTGGGAATCGCCTTa    <  1:2178689/69‑1 (MQ=255)

                                                      aTCTCGTCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCGGTAGCATCTCTTTGGGAATCGCCTTa    <  1:2396689/69‑1 (MQ=255)

                                                      aTCTCGTCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCGGTAGCATCTCTTTGGGAATCGCCTTa    <  1:2771730/69‑1 (MQ=255)

                                                      aTCTCGTCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCGGTAGCATCTCTTTGGGAATCGCCTTa    <  1:247057/69‑1 (MQ=255)

                                                      aTCTCGTCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCGGTAGCATCTCTTTGGGAATCGCCTTa    <  1:2416301/69‑1 (MQ=255)

                                                      aTCTCGTCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCGGTAGCATCTCTTTGGGAATCGCCTTa    <  1:3194939/69‑1 (MQ=255)

                                                         tcGTCAAC‑AATGTACTTAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTggg              <  1:1305189/56‑1 (MQ=255)

                                                         tcGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTTGTAGCATCTCTTTggg              <  1:3276158/56‑1 (MQ=255)

                                                         tcGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTggg              <  1:1456931/56‑1 (MQ=255)

                                                         tcGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTggg              <  1:2340839/56‑1 (MQ=255)

                                                         tcGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTggg              <  1:423569/56‑1 (MQ=255)

                                                         tcGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTggg              <  1:18846/56‑1 (MQ=255)

                                                         tcGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTggg              <  1:100249/56‑1 (MQ=255)

                                                         tcGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTggg              <  1:1683604/56‑1 (MQ=255)

                                                         tcGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTggg              <  1:3032487/56‑1 (MQ=255)

                                                         tcGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCTTAGt  >  1:3341716/1‑68 (MQ=255)

                                                         tcGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGAATGGTAGCATCTCTTTggg              <  1:1759437/56‑1 (MQ=255)

                                                            tCAAC‑GATGTACTGAATCATTGGGTTGTCGACGATCgg                             >  1:3250244/1‑38 (MQ=25)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:841078/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:1079180/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:887270/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:108491/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:2970916/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:103793/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:739077/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:1634350/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:1901731/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:1905889/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:2216766/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:3231518/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:3181401/1‑38 (MQ=38)

                                                            tCAAC‑GATGTACTGAATCATTGGCTTGTCGACGATCgg                             >  1:2854158/1‑38 (MQ=38)

GCGTTCTTGGACGCGTGAGTTACCAGGAGGATTTCTTTGATCCCTGCAGCCACAATCTCGTCAAC‑AATGTACTGAATCATTGGCTTGTCGACGATTGGTAGCATCTCTTTGGGTATCGCCTTAGT  >  minE/1322749‑1322873

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A